Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Warning! This can take a few seconds.

      Regex mode off

        Explain with AI

        Configure AI settings to get explanations of plots and data in this report.

        Keys entered here will be stored in your browser's local storage. See the docs.


        Anonymize samples off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
        Settings are automatically saved. You can also save named configurations below.

        Save Settings

        You can save the toolbox settings for this report to the browser or as a file.


        Load Settings

        Choose a saved report profile from the browser or load from a file:

          Load from File

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.29

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2025-08-01, 13:40 AEST based on data in: /raid/VIDRL-USERS/HOME/aduncan/projects/nf-pipeline/work/5f/f8d8d5fbedd460b78ebd9b4d8448c0

        Because this report contains a lot of samples, you may need to click 'Show plot' to see some graphs.

        General Statistics

        Showing 221/221 rows and 22/41 columns.
        Sample Name% rRNAdupInt5'-3' biasM AlignedExonicIntronicIntergenicOverlapping ExonProper PairsError rateNon-primaryReads mapped% Mapped% Proper pairs% MapQ 0 readsTotal seqsMean insertReadsReads mapped% Reads mappedTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedM Unique Reads% Pass DedupDupsGCAvg lenMedian lenFailedSeqsTrimmed basesDupsGCAvg lenMedian lenFailedSeqs
        DW-63-V01__RNA__S_S49
        0.0
        0.0
        nan
        0.1M
        0.0M
        0.1M
        0.1M
        0.0M
        75.6%
        1.63%
        0.0M
        0.2M
        100.0%
        100.0%
        2.0%
        0.2M
        347.3bp
        0.3M
        0.3M
        100.0%
        2.1M
        0.4M
        20.4%
        0.4M
        18.8%
        0.0M
        0.0M
        28.7%
        DW-63-V01__RNA__S_S49_1
        89.8%
        75.0%
        151bp
        151bp
        45%
        9.6M
        82.1%
        77.9%
        53.0%
        124bp
        142bp
        45%
        2.1M
        DW-63-V01__RNA__S_S49_2
        96.0%
        88.0%
        151bp
        151bp
        45%
        9.6M
        7.5%
        85.0%
        56.0%
        123bp
        137bp
        45%
        2.1M
        DW-63-V02__RNA__S_S50
        0.79%
        0.0M
        0.0M
        100.0%
        100.0%
        1.8%
        0.0M
        255.8bp
        0.0M
        0.0M
        100.0%
        0.2M
        0.0M
        4.1%
        0.0M
        3.7%
        0.0M
        0.0M
        36.4%
        DW-63-V02__RNA__S_S50_1
        83.8%
        80.0%
        151bp
        151bp
        45%
        3.6M
        95.5%
        38.4%
        74.0%
        127bp
        151bp
        45%
        0.2M
        DW-63-V02__RNA__S_S50_2
        98.8%
        96.0%
        151bp
        151bp
        55%
        3.6M
        5.6%
        90.4%
        86.0%
        123bp
        151bp
        45%
        0.2M
        DW-63-V03__RNA__S_S51_1
        86.1%
        43.0%
        151bp
        151bp
        55%
        0.0M
        12.5%
        89.3%
        39.0%
        141bp
        151bp
        45%
        0.0M
        DW-63-V03__RNA__S_S51_2
        88.3%
        45.0%
        151bp
        151bp
        55%
        0.0M
        6.3%
        87.9%
        40.0%
        141bp
        151bp
        45%
        0.0M
        DW-63-V04__RNA__S_S52
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        43.9%
        1.78%
        0.0M
        0.0M
        100.0%
        100.0%
        6.3%
        0.0M
        368.7bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        6.3%
        0.0M
        5.6%
        0.0M
        0.0M
        35.5%
        DW-63-V04__RNA__S_S52_1
        55.7%
        77.0%
        151bp
        151bp
        45%
        0.3M
        89.6%
        75.1%
        58.0%
        86bp
        72bp
        55%
        0.1M
        DW-63-V04__RNA__S_S52_2
        96.8%
        91.0%
        151bp
        151bp
        45%
        0.3M
        11.8%
        89.0%
        64.0%
        86bp
        72bp
        55%
        0.1M
        DW-63-V05__RNA__S_S53
        0.1
        0.0
        nan
        0.2M
        0.0M
        0.1M
        0.2M
        0.0M
        66.8%
        2.27%
        0.1M
        0.4M
        100.0%
        100.0%
        3.2%
        0.4M
        615.7bp
        0.5M
        0.5M
        100.0%
        2.9M
        1.3M
        45.6%
        1.2M
        42.1%
        0.1M
        0.3M
        15.8%
        DW-63-V05__RNA__S_S53_1
        84.8%
        61.0%
        151bp
        151bp
        45%
        4.8M
        47.9%
        84.0%
        47.0%
        131bp
        147bp
        27%
        2.9M
        DW-63-V05__RNA__S_S53_2
        89.2%
        69.0%
        151bp
        151bp
        45%
        4.8M
        9.9%
        83.2%
        49.0%
        130bp
        147bp
        36%
        2.9M
        DW-63-V07__RNA__S_S49
        0.4
        0.0
        nan
        0.1M
        0.0M
        0.0M
        0.0M
        0.0M
        68.2%
        1.78%
        0.0M
        0.1M
        100.0%
        100.0%
        2.7%
        0.1M
        711.7bp
        0.1M
        0.1M
        100.0%
        1.0M
        0.5M
        53.5%
        0.5M
        49.9%
        0.0M
        0.1M
        11.4%
        DW-63-V07__RNA__S_S49_1
        84.1%
        71.0%
        151bp
        151bp
        36%
        3.1M
        73.7%
        81.4%
        51.0%
        122bp
        132bp
        27%
        1.0M
        DW-63-V07__RNA__S_S49_2
        95.0%
        85.0%
        151bp
        151bp
        55%
        3.1M
        6.7%
        87.1%
        53.0%
        121bp
        132bp
        55%
        1.0M
        DW-63-V08__RNA__S_S50
        0.0
        0.0
        inf
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        34.3%
        2.68%
        0.0M
        0.0M
        100.0%
        100.0%
        6.7%
        0.0M
        1248.8bp
        0.0M
        0.0M
        100.0%
        0.2M
        0.0M
        19.0%
        0.0M
        16.1%
        0.0M
        0.0M
        8.4%
        DW-63-V08__RNA__S_S50_1
        74.2%
        57.0%
        151bp
        151bp
        45%
        0.3M
        41.0%
        86.0%
        47.0%
        120bp
        137bp
        45%
        0.2M
        DW-63-V08__RNA__S_S50_2
        85.9%
        63.0%
        151bp
        151bp
        55%
        0.3M
        16.5%
        82.9%
        48.0%
        119bp
        137bp
        55%
        0.2M
        DW-63-V09__RNA__S_S51
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        58.5%
        1.36%
        0.0M
        0.0M
        100.0%
        100.0%
        5.0%
        0.0M
        403.1bp
        0.1M
        0.1M
        100.0%
        1.0M
        0.1M
        9.0%
        0.1M
        8.0%
        0.0M
        0.0M
        26.1%
        DW-63-V09__RNA__S_S51_1
        78.5%
        71.0%
        151bp
        151bp
        36%
        2.9M
        73.5%
        71.7%
        51.0%
        117bp
        127bp
        27%
        1.0M
        DW-63-V09__RNA__S_S51_2
        91.2%
        84.0%
        151bp
        151bp
        55%
        2.9M
        8.2%
        76.8%
        53.0%
        117bp
        127bp
        45%
        1.0M
        DW-63-V10__RNA__S_S52
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        84.0%
        0.90%
        0.0M
        0.0M
        100.0%
        100.0%
        1.2%
        0.0M
        370.5bp
        0.1M
        0.1M
        100.0%
        0.4M
        0.2M
        48.8%
        0.2M
        47.0%
        0.0M
        0.0M
        12.6%
        DW-63-V10__RNA__S_S52_1
        78.4%
        75.0%
        151bp
        151bp
        36%
        2.0M
        81.6%
        76.5%
        54.0%
        127bp
        151bp
        45%
        0.4M
        DW-63-V10__RNA__S_S52_2
        95.9%
        90.0%
        151bp
        151bp
        55%
        2.0M
        4.1%
        84.9%
        57.0%
        126bp
        147bp
        55%
        0.4M
        DW-63-V13__RNA__S_S55
        0.3
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        68.4%
        1.28%
        0.0M
        0.0M
        100.0%
        100.0%
        2.7%
        0.0M
        299.7bp
        0.0M
        0.0M
        100.0%
        0.4M
        0.0M
        5.7%
        0.0M
        5.2%
        0.0M
        0.0M
        22.8%
        DW-63-V13__RNA__S_S55_1
        91.3%
        80.0%
        151bp
        151bp
        45%
        6.8M
        95.4%
        53.7%
        71.0%
        109bp
        151bp
        55%
        0.4M
        DW-63-V13__RNA__S_S55_2
        98.9%
        95.0%
        151bp
        151bp
        45%
        6.8M
        6.2%
        92.4%
        81.0%
        106bp
        142bp
        55%
        0.4M
        DW-63-V15__RNA__S_S57
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        18.7%
        1.34%
        0.1M
        0.0M
        100.0%
        100.0%
        18.5%
        0.0M
        89.0bp
        0.1M
        0.1M
        100.0%
        0.6M
        0.1M
        26.0%
        0.1M
        20.4%
        0.0M
        0.0M
        10.5%
        DW-63-V15__RNA__S_S57_1
        81.9%
        71.0%
        151bp
        151bp
        55%
        2.5M
        84.4%
        83.7%
        33.0%
        106bp
        107bp
        55%
        0.6M
        DW-63-V15__RNA__S_S57_2
        95.7%
        85.0%
        151bp
        151bp
        45%
        2.5M
        9.9%
        92.2%
        39.0%
        106bp
        107bp
        45%
        0.6M
        DW-63-V17__RNA__S_S59
        0.0
        0.0
        0.00
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        50.4%
        1.85%
        0.0M
        0.0M
        100.0%
        100.0%
        4.0%
        0.0M
        365.0bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        10.9%
        0.0M
        9.6%
        0.0M
        0.0M
        16.2%
        DW-63-V17__RNA__S_S59_1
        67.7%
        78.0%
        151bp
        151bp
        45%
        0.9M
        86.1%
        70.9%
        67.0%
        128bp
        151bp
        55%
        0.1M
        DW-63-V17__RNA__S_S59_2
        96.1%
        92.0%
        151bp
        151bp
        45%
        0.9M
        6.4%
        81.4%
        71.0%
        126bp
        151bp
        45%
        0.1M
        DW-63-V18__RNA__S_S60
        3.00%
        0.0M
        0.0M
        100.0%
        100.0%
        16.2%
        0.0M
        287.5bp
        0.0M
        0.0M
        100.0%
        0.3M
        0.0M
        7.6%
        0.0M
        4.6%
        0.0M
        0.0M
        51.2%
        DW-63-V18__RNA__S_S60_1
        80.5%
        78.0%
        151bp
        151bp
        45%
        3.2M
        93.0%
        62.3%
        51.0%
        124bp
        151bp
        55%
        0.3M
        DW-63-V18__RNA__S_S60_2
        98.3%
        93.0%
        151bp
        151bp
        45%
        3.2M
        5.0%
        87.9%
        59.0%
        121bp
        147bp
        45%
        0.3M
        DW-63-V19__RNA__S_S55
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        56.9%
        1.18%
        0.0M
        0.0M
        100.0%
        100.0%
        4.0%
        0.0M
        236.1bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        9.7%
        0.0M
        8.9%
        0.0M
        0.0M
        13.5%
        DW-63-V19__RNA__S_S55_1
        70.1%
        78.0%
        151bp
        151bp
        36%
        1.0M
        90.5%
        66.0%
        66.0%
        114bp
        137bp
        45%
        0.1M
        DW-63-V19__RNA__S_S55_2
        97.6%
        96.0%
        151bp
        151bp
        55%
        1.0M
        3.5%
        88.5%
        73.0%
        114bp
        137bp
        55%
        0.1M
        DW-63-V20__RNA__S_S56
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        37.7%
        3.16%
        0.0M
        0.0M
        100.0%
        100.0%
        5.1%
        0.0M
        347.3bp
        0.0M
        0.0M
        100.0%
        0.2M
        0.0M
        13.3%
        0.0M
        10.9%
        0.0M
        0.0M
        21.2%
        DW-63-V20__RNA__S_S56_1
        71.3%
        72.0%
        151bp
        151bp
        45%
        0.6M
        64.7%
        85.1%
        65.0%
        123bp
        147bp
        45%
        0.2M
        DW-63-V20__RNA__S_S56_2
        86.6%
        83.0%
        151bp
        151bp
        55%
        0.6M
        9.5%
        77.3%
        63.0%
        122bp
        147bp
        55%
        0.2M
        DW-63-V21__RNA__S_S57
        0.8
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        61.6%
        1.14%
        0.0M
        0.0M
        100.0%
        100.0%
        3.3%
        0.0M
        304.9bp
        0.0M
        0.0M
        100.0%
        0.2M
        0.0M
        8.6%
        0.0M
        7.7%
        0.0M
        0.0M
        11.9%
        DW-63-V21__RNA__S_S57_1
        79.4%
        78.0%
        151bp
        151bp
        36%
        1.6M
        91.6%
        69.4%
        65.0%
        102bp
        102bp
        45%
        0.2M
        DW-63-V21__RNA__S_S57_2
        98.1%
        95.0%
        151bp
        151bp
        55%
        1.6M
        4.5%
        90.8%
        72.0%
        102bp
        102bp
        55%
        0.2M
        DW-63-V22__RNA__S_S58
        0.0
        0.0
        2.65
        0.6M
        0.2M
        0.5M
        0.5M
        0.0M
        80.7%
        1.24%
        0.2M
        1.2M
        100.0%
        100.0%
        1.2%
        1.2M
        370.0bp
        1.4M
        1.4M
        100.0%
        37.7M
        5.6M
        14.8%
        5.3M
        13.9%
        0.3M
        0.7M
        11.2%
        DW-63-V22__RNA__S_S58_1
        95.6%
        53.0%
        151bp
        151bp
        27%
        40.5M
        20.3%
        96.1%
        51.0%
        129bp
        142bp
        18%
        37.7M
        DW-63-V22__RNA__S_S58_2
        94.8%
        55.0%
        151bp
        151bp
        45%
        40.5M
        13.8%
        94.8%
        51.0%
        129bp
        142bp
        36%
        37.7M
        DW-63-V24__RNA__S_S60
        0.99%
        0.0M
        0.0M
        100.0%
        100.0%
        4.5%
        0.0M
        261.8bp
        0.0M
        0.0M
        100.0%
        0.3M
        0.0M
        4.2%
        0.0M
        3.1%
        0.0M
        0.0M
        36.2%
        DW-63-V24__RNA__S_S60_1
        85.4%
        80.0%
        151bp
        151bp
        36%
        4.1M
        94.8%
        40.7%
        73.0%
        118bp
        151bp
        36%
        0.3M
        DW-63-V24__RNA__S_S60_2
        98.7%
        98.0%
        151bp
        151bp
        55%
        4.1M
        2.2%
        92.9%
        88.0%
        118bp
        151bp
        55%
        0.3M
        DW-63-V26__RNA__S_S62
        0.1
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        68.4%
        1.28%
        0.0M
        0.0M
        100.0%
        100.0%
        2.3%
        0.0M
        376.5bp
        0.0M
        0.0M
        100.0%
        0.6M
        0.1M
        9.8%
        0.1M
        8.9%
        0.0M
        0.0M
        14.9%
        DW-63-V26__RNA__S_S62_1
        86.5%
        79.0%
        151bp
        151bp
        45%
        5.1M
        90.4%
        70.4%
        66.0%
        117bp
        147bp
        55%
        0.6M
        DW-63-V26__RNA__S_S62_2
        97.2%
        93.0%
        151bp
        151bp
        45%
        5.1M
        7.2%
        86.1%
        70.0%
        115bp
        137bp
        45%
        0.6M
        DW-63-V27__RNA__S_S63
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        38.4%
        1.65%
        0.0M
        0.0M
        100.0%
        100.0%
        4.3%
        0.0M
        475.3bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        6.9%
        0.0M
        5.9%
        0.0M
        0.0M
        23.7%
        DW-63-V27__RNA__S_S63_1
        72.3%
        79.0%
        151bp
        151bp
        45%
        1.6M
        93.3%
        49.7%
        66.0%
        128bp
        151bp
        45%
        0.1M
        DW-63-V27__RNA__S_S63_2
        98.2%
        95.0%
        151bp
        151bp
        55%
        1.6M
        5.7%
        87.6%
        74.0%
        125bp
        151bp
        45%
        0.1M
        DW-63-V28__RNA__S_S64
        0.0
        0.0
        inf
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        20.5%
        2.71%
        0.0M
        0.0M
        100.0%
        100.0%
        12.9%
        0.0M
        1702.6bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        12.3%
        0.0M
        9.6%
        0.0M
        0.0M
        26.6%
        DW-63-V28__RNA__S_S64_1
        61.7%
        76.0%
        151bp
        151bp
        55%
        0.4M
        66.8%
        84.4%
        70.0%
        131bp
        151bp
        55%
        0.1M
        DW-63-V28__RNA__S_S64_2
        86.8%
        86.0%
        151bp
        151bp
        45%
        0.4M
        9.3%
        69.1%
        68.0%
        128bp
        151bp
        45%
        0.1M
        DW-63-V29__RNA__S_S65
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        76.0%
        1.18%
        0.0M
        0.0M
        100.0%
        100.0%
        1.4%
        0.0M
        360.0bp
        0.0M
        0.0M
        100.0%
        0.3M
        0.2M
        53.9%
        0.2M
        51.5%
        0.0M
        0.0M
        12.1%
        DW-63-V29__RNA__S_S65_1
        74.5%
        75.0%
        151bp
        151bp
        45%
        1.4M
        81.0%
        76.9%
        54.0%
        132bp
        151bp
        45%
        0.3M
        DW-63-V29__RNA__S_S65_2
        95.9%
        88.0%
        151bp
        151bp
        45%
        1.4M
        6.7%
        85.4%
        57.0%
        131bp
        151bp
        45%
        0.3M
        DW-63-V30__RNA__S_S66
        4.43%
        0.0M
        0.0M
        100.0%
        100.0%
        13.6%
        0.0M
        1002.2bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        8.6%
        0.0M
        4.5%
        0.0M
        0.0M
        62.6%
        DW-63-V30__RNA__S_S66_1
        65.5%
        77.0%
        151bp
        151bp
        45%
        0.8M
        88.4%
        67.0%
        55.0%
        130bp
        151bp
        55%
        0.1M
        DW-63-V30__RNA__S_S66_2
        96.0%
        92.0%
        151bp
        151bp
        45%
        0.8M
        6.5%
        76.8%
        60.0%
        126bp
        151bp
        45%
        0.1M
        DW-63-V31__RNA__S_S61
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        31.6%
        2.39%
        0.0M
        0.0M
        100.0%
        100.0%
        6.9%
        0.0M
        323.1bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        10.2%
        0.0M
        8.1%
        0.0M
        0.0M
        13.2%
        DW-63-V31__RNA__S_S61_1
        55.4%
        75.0%
        151bp
        151bp
        45%
        0.4M
        79.4%
        75.2%
        59.0%
        124bp
        151bp
        45%
        0.1M
        DW-63-V31__RNA__S_S61_2
        92.1%
        89.0%
        151bp
        151bp
        55%
        0.4M
        5.2%
        72.5%
        60.0%
        123bp
        147bp
        55%
        0.1M
        DW-63-V32__RNA__S_S62
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        15.9%
        2.42%
        0.0M
        0.0M
        100.0%
        100.0%
        14.0%
        0.0M
        103.0bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        13.4%
        0.0M
        9.9%
        0.0M
        0.0M
        6.2%
        DW-63-V32__RNA__S_S62_1
        71.1%
        70.0%
        151bp
        151bp
        45%
        0.2M
        38.7%
        84.4%
        68.0%
        129bp
        151bp
        45%
        0.1M
        DW-63-V32__RNA__S_S62_2
        76.9%
        75.0%
        151bp
        151bp
        55%
        0.2M
        12.3%
        70.2%
        65.0%
        128bp
        151bp
        55%
        0.1M
        DW-63-V34__RNA__S_S64
        0.0
        0.0
        inf
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        42.7%
        2.46%
        0.0M
        0.0M
        100.0%
        100.0%
        5.4%
        0.0M
        600.2bp
        0.0M
        0.0M
        100.0%
        0.2M
        0.0M
        16.6%
        0.0M
        14.0%
        0.0M
        0.0M
        8.4%
        DW-63-V34__RNA__S_S64_1
        62.9%
        75.0%
        151bp
        151bp
        45%
        0.5M
        68.7%
        81.6%
        66.0%
        129bp
        151bp
        45%
        0.2M
        DW-63-V34__RNA__S_S64_2
        88.1%
        86.0%
        151bp
        151bp
        55%
        0.5M
        6.7%
        70.8%
        64.0%
        127bp
        151bp
        55%
        0.2M
        DW-63-V35__RNA__S_S65
        0.0
        0.0
        1.33
        0.9M
        0.7M
        0.3M
        0.6M
        0.1M
        78.4%
        1.80%
        0.2M
        1.8M
        100.0%
        100.0%
        0.2%
        1.8M
        581.9bp
        2.0M
        2.0M
        100.0%
        8.6M
        4.4M
        51.2%
        4.0M
        46.1%
        0.4M
        1.0M
        20.5%
        DW-63-V35__RNA__S_S65_1
        91.7%
        62.0%
        151bp
        151bp
        45%
        9.2M
        26.8%
        93.6%
        63.0%
        117bp
        122bp
        27%
        8.6M
        DW-63-V35__RNA__S_S65_2
        91.6%
        66.0%
        151bp
        151bp
        55%
        9.2M
        21.3%
        91.7%
        64.0%
        118bp
        122bp
        36%
        8.6M
        DW-63-V36__RNA__S_S66
        0.7
        0.0
        0.00
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        72.7%
        2.11%
        0.0M
        0.0M
        100.0%
        100.0%
        2.4%
        0.0M
        298.4bp
        0.0M
        0.0M
        100.0%
        0.3M
        0.1M
        38.7%
        0.1M
        36.0%
        0.0M
        0.0M
        11.8%
        DW-63-V36__RNA__S_S66_1
        65.4%
        68.0%
        151bp
        151bp
        45%
        0.5M
        57.7%
        83.6%
        55.0%
        126bp
        137bp
        45%
        0.3M
        DW-63-V36__RNA__S_S66_2
        89.5%
        77.0%
        151bp
        151bp
        55%
        0.5M
        9.2%
        81.1%
        55.0%
        125bp
        137bp
        55%
        0.3M
        DW-63-V37__RNA__S_S67
        1.57%
        0.0M
        0.0M
        100.0%
        100.0%
        17.6%
        0.0M
        174.2bp
        0.0M
        0.0M
        100.0%
        0.4M
        0.0M
        5.0%
        0.0M
        3.3%
        0.0M
        0.0M
        27.5%
        DW-63-V37__RNA__S_S67_1
        88.7%
        79.0%
        151bp
        151bp
        45%
        4.0M
        93.3%
        72.1%
        59.0%
        106bp
        127bp
        55%
        0.4M
        DW-63-V37__RNA__S_S67_2
        98.5%
        94.0%
        151bp
        151bp
        45%
        4.0M
        6.7%
        91.8%
        66.0%
        104bp
        117bp
        45%
        0.4M
        DW-63-V38__RNA__S_S68
        0.0
        0.0
        24.71
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        46.5%
        2.33%
        0.0M
        0.1M
        100.0%
        100.0%
        4.2%
        0.1M
        555.4bp
        0.1M
        0.1M
        100.0%
        0.7M
        0.2M
        21.9%
        0.1M
        19.2%
        0.0M
        0.1M
        30.0%
        DW-63-V38__RNA__S_S68_1
        87.9%
        75.0%
        151bp
        151bp
        45%
        4.5M
        87.5%
        71.4%
        56.0%
        123bp
        147bp
        45%
        0.7M
        DW-63-V38__RNA__S_S68_2
        92.4%
        91.0%
        151bp
        151bp
        45%
        4.5M
        7.6%
        83.8%
        62.0%
        122bp
        147bp
        45%
        0.7M
        DW-63-V40__RNA__S_S70
        0.0
        0.0
        inf
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        22.1%
        2.79%
        0.0M
        0.0M
        100.0%
        100.0%
        12.3%
        0.0M
        434.6bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        20.6%
        0.0M
        17.3%
        0.0M
        0.0M
        11.1%
        DW-63-V40__RNA__S_S70_1
        63.2%
        72.0%
        151bp
        151bp
        55%
        0.3M
        63.8%
        82.7%
        60.0%
        124bp
        151bp
        55%
        0.1M
        DW-63-V40__RNA__S_S70_2
        88.8%
        82.0%
        151bp
        151bp
        45%
        0.3M
        11.4%
        78.2%
        62.0%
        123bp
        151bp
        45%
        0.1M
        DW-63-V41__RNA__S_S71
        0.0
        0.0
        inf
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        21.7%
        3.27%
        0.0M
        0.0M
        100.0%
        100.0%
        8.4%
        0.0M
        672.1bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        10.6%
        0.0M
        8.0%
        0.0M
        0.0M
        39.0%
        DW-63-V41__RNA__S_S71_1
        68.3%
        77.0%
        151bp
        151bp
        45%
        0.8M
        86.9%
        71.9%
        54.0%
        129bp
        151bp
        55%
        0.1M
        DW-63-V41__RNA__S_S71_2
        96.1%
        91.0%
        151bp
        151bp
        45%
        0.8M
        6.3%
        79.8%
        58.0%
        126bp
        147bp
        45%
        0.1M
        DW-63-V44__RNA__S_S68
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        38.6%
        2.55%
        0.1M
        0.1M
        100.0%
        100.0%
        8.3%
        0.1M
        474.1bp
        0.2M
        0.2M
        100.0%
        0.8M
        0.3M
        35.5%
        0.3M
        31.7%
        0.0M
        0.1M
        26.1%
        DW-63-V44__RNA__S_S68_1
        76.8%
        66.0%
        151bp
        151bp
        45%
        1.6M
        55.0%
        85.5%
        52.0%
        131bp
        147bp
        27%
        0.8M
        DW-63-V44__RNA__S_S68_2
        88.7%
        75.0%
        151bp
        151bp
        55%
        1.6M
        7.7%
        80.4%
        52.0%
        130bp
        147bp
        45%
        0.8M
        DW-63-V45__RNA__S_S69
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        53.7%
        1.43%
        0.0M
        0.0M
        100.0%
        100.0%
        3.5%
        0.0M
        1008.2bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.1M
        44.6%
        0.1M
        41.5%
        0.0M
        0.0M
        14.1%
        DW-63-V45__RNA__S_S69_1
        62.6%
        74.0%
        151bp
        151bp
        36%
        0.5M
        76.7%
        78.7%
        55.0%
        128bp
        147bp
        45%
        0.1M
        DW-63-V45__RNA__S_S69_2
        94.8%
        88.0%
        151bp
        151bp
        55%
        0.5M
        4.7%
        84.5%
        58.0%
        128bp
        147bp
        55%
        0.1M
        DW-63-V46__RNA__S_S70
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        13.4%
        4.20%
        0.1M
        0.0M
        100.0%
        100.0%
        18.5%
        0.0M
        2964.9bp
        0.1M
        0.1M
        100.0%
        0.4M
        0.0M
        10.1%
        0.0M
        5.3%
        0.0M
        0.1M
        62.2%
        DW-63-V46__RNA__S_S70_1
        70.2%
        61.0%
        151bp
        151bp
        45%
        0.8M
        59.3%
        82.6%
        39.0%
        125bp
        151bp
        45%
        0.4M
        DW-63-V46__RNA__S_S70_2
        87.2%
        71.0%
        151bp
        151bp
        55%
        0.8M
        9.8%
        76.0%
        38.0%
        123bp
        147bp
        55%
        0.4M
        DW-63-V47__RNA__S_S71
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        70.4%
        1.80%
        0.0M
        0.0M
        100.0%
        100.0%
        2.3%
        0.0M
        312.6bp
        0.1M
        0.1M
        100.0%
        0.6M
        0.3M
        51.7%
        0.3M
        48.8%
        0.0M
        0.0M
        8.1%
        DW-63-V47__RNA__S_S71_1
        76.2%
        65.0%
        151bp
        151bp
        36%
        1.0M
        59.2%
        86.6%
        50.0%
        114bp
        117bp
        18%
        0.6M
        DW-63-V47__RNA__S_S71_2
        92.9%
        75.0%
        151bp
        151bp
        55%
        1.0M
        14.0%
        88.5%
        52.0%
        114bp
        117bp
        36%
        0.6M
        DW-63-V48__RNA__S_S72
        0.0
        0.0
        inf
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        70.2%
        1.37%
        0.0M
        0.0M
        100.0%
        100.0%
        2.5%
        0.0M
        284.8bp
        0.0M
        0.0M
        100.0%
        0.2M
        0.1M
        26.3%
        0.1M
        24.2%
        0.0M
        0.0M
        12.0%
        DW-63-V48__RNA__S_S72_1
        76.1%
        78.0%
        151bp
        151bp
        36%
        1.4M
        89.5%
        73.7%
        61.0%
        103bp
        112bp
        45%
        0.2M
        DW-63-V48__RNA__S_S72_2
        97.1%
        94.0%
        151bp
        151bp
        55%
        1.4M
        5.6%
        86.8%
        65.0%
        103bp
        112bp
        55%
        0.2M
        DW-63-V49__RNA__S_S73
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        50.4%
        1.20%
        0.0M
        0.0M
        100.0%
        100.0%
        5.5%
        0.0M
        101.9bp
        0.0M
        0.0M
        100.0%
        0.3M
        0.0M
        6.2%
        0.0M
        5.2%
        0.0M
        0.0M
        52.5%
        DW-63-V49__RNA__S_S73_1
        89.9%
        80.0%
        151bp
        151bp
        45%
        6.9M
        95.9%
        22.6%
        75.0%
        137bp
        151bp
        36%
        0.3M
        DW-63-V49__RNA__S_S73_2
        98.4%
        96.0%
        151bp
        151bp
        55%
        6.9M
        5.1%
        89.0%
        88.0%
        132bp
        151bp
        45%
        0.3M
        DW-63-V50__RNA__S_S74
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        43.5%
        1.03%
        0.0M
        0.0M
        100.0%
        100.0%
        7.4%
        0.0M
        141.4bp
        0.0M
        0.0M
        100.0%
        0.3M
        0.0M
        6.2%
        0.0M
        5.2%
        0.0M
        0.0M
        19.7%
        DW-63-V50__RNA__S_S74_1
        79.3%
        79.0%
        151bp
        151bp
        45%
        3.4M
        92.9%
        48.8%
        69.0%
        132bp
        151bp
        36%
        0.3M
        DW-63-V50__RNA__S_S74_2
        95.5%
        94.0%
        151bp
        151bp
        45%
        3.4M
        5.3%
        84.8%
        79.0%
        131bp
        151bp
        45%
        0.3M
        DW-63-V51__RNA__S_S75
        0.0
        0.0
        1.40
        0.6M
        0.2M
        0.6M
        0.3M
        0.0M
        86.0%
        0.84%
        0.1M
        1.1M
        100.0%
        100.0%
        0.8%
        1.1M
        364.3bp
        1.3M
        1.3M
        100.0%
        6.5M
        5.9M
        90.2%
        5.6M
        86.5%
        0.2M
        0.3M
        9.2%
        DW-63-V51__RNA__S_S75_1
        88.0%
        54.0%
        151bp
        151bp
        45%
        8.0M
        27.3%
        89.6%
        48.0%
        134bp
        147bp
        27%
        6.5M
        DW-63-V51__RNA__S_S75_2
        89.6%
        58.0%
        151bp
        151bp
        45%
        8.0M
        10.0%
        87.6%
        48.0%
        134bp
        147bp
        18%
        6.5M
        DW-63-V52__RNA__S_S76
        0.0
        0.0
        inf
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        28.7%
        2.08%
        0.0M
        0.0M
        100.0%
        100.0%
        10.3%
        0.0M
        716.8bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        11.3%
        0.0M
        9.3%
        0.0M
        0.0M
        10.7%
        DW-63-V52__RNA__S_S76_1
        59.5%
        73.0%
        151bp
        151bp
        55%
        0.4M
        71.7%
        78.7%
        57.0%
        131bp
        151bp
        55%
        0.1M
        DW-63-V52__RNA__S_S76_2
        89.3%
        85.0%
        151bp
        151bp
        45%
        0.4M
        8.1%
        71.4%
        59.0%
        130bp
        151bp
        45%
        0.1M
        DW-63-V54__RNA__S_S78
        0.1
        0.0
        nan
        0.2M
        0.0M
        0.2M
        0.2M
        0.0M
        84.7%
        0.92%
        0.1M
        0.5M
        100.0%
        100.0%
        1.1%
        0.5M
        205.2bp
        0.5M
        0.5M
        100.0%
        3.6M
        3.3M
        92.2%
        3.2M
        88.9%
        0.1M
        0.3M
        7.3%
        DW-63-V54__RNA__S_S78_1
        88.1%
        52.0%
        151bp
        151bp
        45%
        4.4M
        26.8%
        87.7%
        45.0%
        135bp
        147bp
        27%
        3.6M
        DW-63-V54__RNA__S_S78_2
        89.6%
        56.0%
        151bp
        151bp
        45%
        4.4M
        9.8%
        87.7%
        46.0%
        135bp
        147bp
        18%
        3.6M
        DW-63-V56__RNA__S_S74
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        29.5%
        1.44%
        0.0M
        0.0M
        100.0%
        100.0%
        11.9%
        0.0M
        105.5bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        12.2%
        0.0M
        10.1%
        0.0M
        0.0M
        21.9%
        DW-63-V56__RNA__S_S74_1
        54.2%
        75.0%
        151bp
        151bp
        45%
        0.2M
        64.9%
        81.4%
        69.0%
        131bp
        151bp
        45%
        0.1M
        DW-63-V56__RNA__S_S74_2
        86.9%
        86.0%
        151bp
        151bp
        55%
        0.2M
        6.3%
        70.8%
        68.0%
        131bp
        151bp
        55%
        0.1M
        DW-63-V57__RNA__S_S75
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        79.5%
        0.78%
        0.0M
        0.1M
        100.0%
        100.0%
        1.6%
        0.1M
        157.4bp
        0.1M
        0.1M
        100.0%
        0.4M
        0.3M
        80.5%
        0.3M
        76.9%
        0.0M
        0.0M
        8.0%
        DW-63-V57__RNA__S_S75_1
        71.0%
        64.0%
        151bp
        151bp
        36%
        0.9M
        57.3%
        85.6%
        47.0%
        128bp
        137bp
        18%
        0.4M
        DW-63-V57__RNA__S_S75_2
        93.3%
        74.0%
        151bp
        151bp
        55%
        0.9M
        7.9%
        87.8%
        48.0%
        128bp
        137bp
        45%
        0.4M
        DW-63-V59__RNA__S_S77
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        49.0%
        1.08%
        0.0M
        0.0M
        100.0%
        100.0%
        5.9%
        0.0M
        300.1bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        17.2%
        0.0M
        13.8%
        0.0M
        0.0M
        11.2%
        DW-63-V59__RNA__S_S77_1
        58.0%
        75.0%
        151bp
        151bp
        45%
        0.4M
        75.1%
        79.4%
        66.0%
        121bp
        142bp
        45%
        0.1M
        DW-63-V59__RNA__S_S77_2
        93.0%
        89.0%
        151bp
        151bp
        55%
        0.4M
        6.9%
        80.6%
        67.0%
        121bp
        142bp
        55%
        0.1M
        DW-63-V60__RNA__S_S78
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        37.1%
        1.01%
        0.0M
        0.0M
        100.0%
        100.0%
        11.6%
        0.0M
        235.9bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        8.0%
        0.0M
        6.8%
        0.0M
        0.0M
        21.4%
        DW-63-V60__RNA__S_S78_1
        62.0%
        79.0%
        151bp
        151bp
        36%
        0.7M
        91.0%
        61.5%
        62.0%
        124bp
        151bp
        45%
        0.1M
        DW-63-V60__RNA__S_S78_2
        97.6%
        96.0%
        151bp
        151bp
        55%
        0.7M
        2.3%
        85.0%
        69.0%
        125bp
        151bp
        55%
        0.1M
        DW-63-V61__RNA__S_S79
        1.36%
        0.0M
        0.0M
        100.0%
        100.0%
        8.6%
        0.0M
        312.7bp
        0.0M
        0.0M
        100.0%
        0.2M
        0.0M
        2.9%
        0.0M
        2.3%
        0.0M
        0.0M
        11.4%
        DW-63-V61__RNA__S_S79_1
        79.2%
        79.0%
        151bp
        151bp
        45%
        2.4M
        93.3%
        63.2%
        69.0%
        104bp
        151bp
        55%
        0.2M
        DW-63-V61__RNA__S_S79_2
        97.9%
        94.0%
        151bp
        151bp
        45%
        2.4M
        7.0%
        93.3%
        79.0%
        103bp
        142bp
        45%
        0.2M
        DW-63-V63__RNA__S_S81
        2.31%
        0.0M
        0.0M
        100.0%
        100.0%
        6.0%
        0.0M
        394.7bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        5.1%
        0.0M
        3.9%
        0.0M
        0.0M
        12.2%
        DW-63-V63__RNA__S_S81_1
        63.6%
        78.0%
        151bp
        151bp
        45%
        0.7M
        93.0%
        47.4%
        63.0%
        133bp
        151bp
        45%
        0.1M
        DW-63-V63__RNA__S_S81_2
        95.4%
        94.0%
        151bp
        151bp
        45%
        0.7M
        5.5%
        81.9%
        72.0%
        131bp
        151bp
        45%
        0.1M
        DW-63-V64__RNA__S_S82
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        44.0%
        1.30%
        0.0M
        0.0M
        100.0%
        100.0%
        8.1%
        0.0M
        109.6bp
        0.0M
        0.0M
        100.0%
        0.0M
        0.0M
        8.3%
        0.0M
        7.0%
        0.0M
        0.0M
        37.2%
        DW-63-V64__RNA__S_S82_1
        48.6%
        79.0%
        151bp
        151bp
        45%
        0.2M
        79.4%
        79.1%
        74.0%
        134bp
        151bp
        55%
        0.0M
        DW-63-V64__RNA__S_S82_2
        91.6%
        91.0%
        151bp
        151bp
        45%
        0.2M
        6.4%
        68.7%
        74.0%
        131bp
        151bp
        45%
        0.0M
        DW-63-V65__RNA__S_S83
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        80.6%
        0.87%
        0.0M
        0.0M
        100.0%
        100.0%
        1.8%
        0.0M
        165.9bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.1M
        63.5%
        0.1M
        61.4%
        0.0M
        0.0M
        7.8%
        DW-63-V65__RNA__S_S83_1
        61.5%
        73.0%
        151bp
        151bp
        45%
        0.5M
        76.3%
        81.9%
        50.0%
        133bp
        147bp
        55%
        0.1M
        DW-63-V65__RNA__S_S83_2
        96.0%
        85.0%
        151bp
        151bp
        45%
        0.5M
        6.4%
        87.7%
        52.0%
        133bp
        147bp
        36%
        0.1M
        DW-63-V66__RNA__S_S84
        0.1
        0.0
        nan
        0.2M
        0.0M
        0.2M
        0.2M
        0.0M
        84.5%
        0.94%
        0.0M
        0.4M
        100.0%
        100.0%
        1.1%
        0.4M
        180.9bp
        0.5M
        0.5M
        100.0%
        3.4M
        3.1M
        92.7%
        3.0M
        89.3%
        0.1M
        0.2M
        6.8%
        DW-63-V66__RNA__S_S84_1
        86.1%
        53.0%
        151bp
        151bp
        36%
        4.0M
        23.9%
        88.6%
        48.0%
        135bp
        147bp
        27%
        3.4M
        DW-63-V66__RNA__S_S84_2
        89.2%
        57.0%
        151bp
        151bp
        36%
        4.0M
        9.8%
        87.7%
        49.0%
        135bp
        147bp
        18%
        3.4M
        DW-63-V67__RNA__S_S79
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        41.8%
        0.77%
        0.0M
        0.0M
        100.0%
        100.0%
        10.0%
        0.0M
        292.5bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        15.4%
        0.0M
        12.7%
        0.0M
        0.0M
        7.4%
        DW-63-V67__RNA__S_S79_1
        59.1%
        77.0%
        151bp
        151bp
        36%
        0.5M
        86.8%
        73.3%
        60.0%
        126bp
        151bp
        45%
        0.1M
        DW-63-V67__RNA__S_S79_2
        96.5%
        94.0%
        151bp
        151bp
        55%
        0.5M
        3.1%
        83.8%
        65.0%
        126bp
        151bp
        55%
        0.1M
        DW-63-V68__RNA__S_S80
        0.0
        0.0
        1.33
        0.7M
        0.3M
        0.7M
        0.4M
        0.0M
        85.8%
        0.82%
        0.1M
        1.5M
        100.0%
        100.0%
        0.7%
        1.5M
        370.6bp
        1.6M
        1.6M
        100.0%
        11.3M
        10.1M
        89.3%
        9.6M
        85.2%
        0.5M
        0.8M
        7.5%
        DW-63-V68__RNA__S_S80_1
        91.6%
        51.0%
        151bp
        151bp
        27%
        11.4M
        13.1%
        92.1%
        50.0%
        133bp
        142bp
        18%
        11.3M
        DW-63-V68__RNA__S_S80_2
        89.8%
        52.0%
        151bp
        151bp
        45%
        11.4M
        12.4%
        90.0%
        50.0%
        132bp
        142bp
        27%
        11.3M
        DW-63-V69__RNA__S_S81
        0.0
        0.0
        0.00
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        22.2%
        3.86%
        0.0M
        0.0M
        100.0%
        100.0%
        14.3%
        0.0M
        3071.7bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        10.4%
        0.0M
        5.2%
        0.0M
        0.0M
        13.6%
        DW-63-V69__RNA__S_S81_1
        58.2%
        71.0%
        151bp
        151bp
        45%
        0.3M
        66.4%
        82.3%
        56.0%
        131bp
        151bp
        45%
        0.1M
        DW-63-V69__RNA__S_S81_2
        87.4%
        81.0%
        151bp
        151bp
        55%
        0.3M
        6.9%
        70.6%
        51.0%
        127bp
        151bp
        55%
        0.1M
        DW-63-V70__RNA__S_S82
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        81.1%
        1.03%
        0.0M
        0.1M
        100.0%
        100.0%
        0.8%
        0.1M
        582.1bp
        0.1M
        0.1M
        100.0%
        0.5M
        0.3M
        57.5%
        0.3M
        54.0%
        0.0M
        0.0M
        8.1%
        DW-63-V70__RNA__S_S82_1
        79.7%
        73.0%
        151bp
        151bp
        36%
        1.8M
        75.5%
        81.3%
        55.0%
        129bp
        147bp
        27%
        0.5M
        DW-63-V70__RNA__S_S82_2
        95.7%
        87.0%
        151bp
        151bp
        55%
        1.8M
        4.5%
        87.3%
        57.0%
        129bp
        147bp
        55%
        0.5M
        DW-63-V72__RNA__S_S84
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        82.0%
        1.43%
        0.0M
        0.0M
        100.0%
        100.0%
        0.8%
        0.0M
        434.4bp
        0.1M
        0.1M
        100.0%
        0.7M
        0.2M
        33.6%
        0.2M
        31.6%
        0.0M
        0.0M
        10.8%
        DW-63-V72__RNA__S_S84_1
        82.3%
        75.0%
        151bp
        151bp
        36%
        2.5M
        77.5%
        83.3%
        64.0%
        119bp
        122bp
        36%
        0.7M
        DW-63-V72__RNA__S_S84_2
        96.5%
        89.0%
        151bp
        151bp
        55%
        2.5M
        6.3%
        89.6%
        66.0%
        119bp
        122bp
        55%
        0.7M
        DW-63-V73__RNA__S_S85
        0.1
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        65.8%
        0.85%
        0.0M
        0.0M
        100.0%
        100.0%
        3.3%
        0.0M
        192.5bp
        0.1M
        0.1M
        100.0%
        0.6M
        0.2M
        34.4%
        0.2M
        31.2%
        0.0M
        0.0M
        9.6%
        DW-63-V73__RNA__S_S85_1
        80.2%
        75.0%
        151bp
        151bp
        45%
        2.6M
        81.4%
        78.3%
        55.0%
        131bp
        151bp
        55%
        0.6M
        DW-63-V73__RNA__S_S85_2
        95.5%
        88.0%
        151bp
        151bp
        45%
        2.6M
        6.4%
        83.5%
        56.0%
        129bp
        147bp
        45%
        0.6M
        DW-63-V75__RNA__S_S87
        0.0
        0.0
        inf
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        33.1%
        3.03%
        0.0M
        0.0M
        100.0%
        100.0%
        6.2%
        0.0M
        2776.0bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        9.8%
        0.0M
        8.2%
        0.0M
        0.0M
        32.1%
        DW-63-V75__RNA__S_S87_1
        66.1%
        78.0%
        151bp
        151bp
        45%
        0.7M
        91.2%
        62.7%
        60.0%
        128bp
        151bp
        55%
        0.1M
        DW-63-V75__RNA__S_S87_2
        96.7%
        93.0%
        151bp
        151bp
        45%
        0.7M
        5.3%
        83.9%
        67.0%
        126bp
        151bp
        45%
        0.1M
        DW-63-V76__RNA__S_S88
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        39.8%
        1.43%
        0.0M
        0.0M
        100.0%
        100.0%
        8.3%
        0.0M
        254.1bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        12.0%
        0.0M
        9.4%
        0.0M
        0.0M
        11.5%
        DW-63-V76__RNA__S_S88_1
        61.2%
        78.0%
        151bp
        151bp
        55%
        0.3M
        62.4%
        86.9%
        76.0%
        136bp
        151bp
        55%
        0.1M
        DW-63-V76__RNA__S_S88_2
        83.4%
        85.0%
        151bp
        151bp
        45%
        0.3M
        8.5%
        64.0%
        71.0%
        132bp
        151bp
        45%
        0.1M
        DW-63-V77__RNA__S_S89
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        61.8%
        1.93%
        0.0M
        0.0M
        100.0%
        100.0%
        4.3%
        0.0M
        151.4bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        8.7%
        0.0M
        6.5%
        0.0M
        0.0M
        14.8%
        DW-63-V77__RNA__S_S89_1
        55.2%
        80.0%
        151bp
        151bp
        55%
        0.4M
        86.9%
        70.6%
        74.0%
        136bp
        151bp
        55%
        0.1M
        DW-63-V77__RNA__S_S89_2
        95.0%
        93.0%
        151bp
        151bp
        55%
        0.4M
        6.2%
        73.0%
        76.0%
        132bp
        151bp
        45%
        0.1M
        DW-63-V78__RNA__S_S90
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        57.2%
        1.10%
        0.0M
        0.0M
        100.0%
        100.0%
        5.9%
        0.0M
        115.3bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        7.9%
        0.0M
        6.8%
        0.0M
        0.0M
        14.7%
        DW-63-V78__RNA__S_S90_1
        60.3%
        80.0%
        151bp
        151bp
        45%
        0.6M
        92.8%
        52.5%
        68.0%
        132bp
        151bp
        55%
        0.1M
        DW-63-V78__RNA__S_S90_2
        97.9%
        95.0%
        151bp
        151bp
        55%
        0.6M
        5.1%
        87.4%
        77.0%
        129bp
        151bp
        45%
        0.1M
        DW-63-V80__RNA__S_S86
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        76.8%
        0.78%
        0.0M
        0.0M
        100.0%
        100.0%
        2.1%
        0.0M
        143.1bp
        0.0M
        0.0M
        100.0%
        0.2M
        0.1M
        50.5%
        0.1M
        48.0%
        0.0M
        0.0M
        6.5%
        DW-63-V80__RNA__S_S86_1
        75.9%
        63.0%
        151bp
        151bp
        45%
        0.3M
        37.4%
        88.9%
        57.0%
        128bp
        142bp
        45%
        0.2M
        DW-63-V80__RNA__S_S86_2
        84.5%
        67.0%
        151bp
        151bp
        55%
        0.3M
        12.8%
        80.8%
        55.0%
        127bp
        142bp
        55%
        0.2M
        DW-63-V82__RNA__S_S88
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        53.5%
        0.99%
        0.0M
        0.0M
        100.0%
        100.0%
        4.9%
        0.0M
        345.5bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        11.9%
        0.0M
        9.6%
        0.0M
        0.0M
        13.1%
        DW-63-V82__RNA__S_S88_1
        63.4%
        77.0%
        151bp
        151bp
        45%
        0.5M
        78.0%
        78.6%
        68.0%
        128bp
        151bp
        45%
        0.1M
        DW-63-V82__RNA__S_S88_2
        92.9%
        91.0%
        151bp
        151bp
        55%
        0.5M
        4.8%
        76.5%
        69.0%
        127bp
        151bp
        55%
        0.1M
        DW-63-V83__RNA__S_S89
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        66.5%
        1.02%
        0.0M
        0.0M
        100.0%
        100.0%
        2.9%
        0.0M
        290.6bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        24.1%
        0.0M
        22.5%
        0.0M
        0.0M
        6.4%
        DW-63-V83__RNA__S_S89_1
        59.6%
        71.0%
        151bp
        151bp
        36%
        0.4M
        70.3%
        81.5%
        55.0%
        123bp
        142bp
        45%
        0.1M
        DW-63-V83__RNA__S_S89_2
        93.4%
        84.0%
        151bp
        151bp
        55%
        0.4M
        7.2%
        84.7%
        56.0%
        123bp
        142bp
        55%
        0.1M
        DW-63-V84__RNA__S_S90
        0.0
        0.0
        inf
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        42.3%
        1.12%
        0.0M
        0.0M
        100.0%
        100.0%
        6.4%
        0.0M
        291.3bp
        0.0M
        0.0M
        100.0%
        0.2M
        0.0M
        8.7%
        0.0M
        7.0%
        0.0M
        0.0M
        12.6%
        DW-63-V84__RNA__S_S90_1
        76.4%
        78.0%
        151bp
        151bp
        36%
        1.4M
        90.1%
        75.5%
        62.0%
        100bp
        102bp
        45%
        0.2M
        DW-63-V84__RNA__S_S90_2
        97.5%
        94.0%
        151bp
        151bp
        55%
        1.4M
        5.7%
        89.2%
        67.0%
        100bp
        102bp
        55%
        0.2M
        DW-63-V85__RNA__S_S91
        2.74%
        0.0M
        0.0M
        100.0%
        100.0%
        4.0%
        0.0M
        248.8bp
        0.0M
        0.0M
        100.0%
        0.5M
        0.0M
        2.5%
        0.0M
        2.0%
        0.0M
        0.0M
        31.0%
        DW-63-V85__RNA__S_S91_1
        92.5%
        81.0%
        151bp
        151bp
        45%
        9.4M
        95.0%
        53.1%
        77.0%
        131bp
        151bp
        55%
        0.5M
        DW-63-V85__RNA__S_S91_2
        99.0%
        96.0%
        151bp
        151bp
        55%
        9.4M
        5.9%
        94.1%
        90.0%
        126bp
        151bp
        45%
        0.5M
        DW-63-V86__RNA__S_S92
        0.0
        0.0
        11.04
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        74.1%
        0.93%
        0.0M
        0.0M
        100.0%
        100.0%
        2.3%
        0.0M
        192.9bp
        0.0M
        0.0M
        100.0%
        0.4M
        0.1M
        30.4%
        0.1M
        28.3%
        0.0M
        0.0M
        8.0%
        DW-63-V86__RNA__S_S92_1
        77.9%
        73.0%
        151bp
        151bp
        45%
        1.5M
        75.7%
        81.0%
        53.0%
        132bp
        151bp
        45%
        0.4M
        DW-63-V86__RNA__S_S92_2
        95.4%
        85.0%
        151bp
        151bp
        45%
        1.5M
        7.5%
        86.7%
        55.0%
        131bp
        147bp
        36%
        0.4M
        DW-63-V87__RNA__S_S93
        0.89%
        0.0M
        0.0M
        100.0%
        100.0%
        8.0%
        0.0M
        236.8bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        4.4%
        0.0M
        3.9%
        0.0M
        0.0M
        26.1%
        DW-63-V87__RNA__S_S93_1
        80.2%
        80.0%
        151bp
        151bp
        45%
        1.9M
        94.9%
        47.3%
        73.0%
        132bp
        151bp
        36%
        0.1M
        DW-63-V87__RNA__S_S93_2
        98.9%
        95.0%
        151bp
        151bp
        45%
        1.9M
        4.6%
        92.4%
        84.0%
        128bp
        151bp
        45%
        0.1M
        DW-63-V89__RNA__S_S95
        1.86%
        0.0M
        0.0M
        100.0%
        100.0%
        6.8%
        0.0M
        284.7bp
        0.0M
        0.0M
        100.0%
        0.3M
        0.0M
        5.7%
        0.0M
        4.6%
        0.0M
        0.0M
        10.5%
        DW-63-V89__RNA__S_S95_1
        80.5%
        77.0%
        151bp
        151bp
        45%
        1.5M
        90.9%
        81.2%
        57.0%
        80bp
        62bp
        55%
        0.3M
        DW-63-V89__RNA__S_S95_2
        96.9%
        91.0%
        151bp
        151bp
        45%
        1.5M
        12.8%
        90.9%
        61.0%
        80bp
        62bp
        45%
        0.3M
        DW-63-V90__RNA__S_S96
        1.09%
        0.0M
        0.0M
        100.0%
        100.0%
        4.6%
        0.0M
        281.8bp
        0.0M
        0.0M
        100.0%
        2.4M
        0.0M
        0.4%
        0.0M
        0.4%
        0.0M
        0.0M
        18.2%
        DW-63-V90__RNA__S_S96_1
        86.4%
        61.0%
        151bp
        151bp
        45%
        3.7M
        43.3%
        92.8%
        50.0%
        134bp
        147bp
        27%
        2.4M
        DW-63-V90__RNA__S_S96_2
        94.8%
        67.0%
        151bp
        151bp
        45%
        3.7M
        8.5%
        93.0%
        50.0%
        134bp
        147bp
        36%
        2.4M
        DW-63-V91__RNA__S_S91
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        42.7%
        0.89%
        0.0M
        0.0M
        100.0%
        100.0%
        9.2%
        0.0M
        98.4bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        8.5%
        0.0M
        7.0%
        0.0M
        0.0M
        18.5%
        DW-63-V91__RNA__S_S91_1
        73.7%
        79.0%
        151bp
        151bp
        36%
        1.1M
        93.1%
        63.9%
        67.0%
        114bp
        147bp
        45%
        0.1M
        DW-63-V91__RNA__S_S91_2
        98.2%
        97.0%
        151bp
        151bp
        55%
        1.1M
        2.5%
        88.3%
        75.0%
        114bp
        147bp
        55%
        0.1M
        DW-63-V92__RNA__S_S92
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        80.7%
        0.82%
        0.0M
        0.0M
        100.0%
        100.0%
        1.3%
        0.0M
        204.5bp
        0.0M
        0.0M
        100.0%
        0.0M
        0.0M
        17.4%
        0.0M
        16.7%
        0.0M
        0.0M
        18.0%
        DW-63-V92__RNA__S_S92_1
        50.3%
        80.0%
        151bp
        151bp
        36%
        0.4M
        94.3%
        47.6%
        62.0%
        141bp
        151bp
        36%
        0.0M
        DW-63-V92__RNA__S_S92_2
        98.0%
        97.0%
        151bp
        151bp
        55%
        0.4M
        0.7%
        84.2%
        71.0%
        141bp
        151bp
        55%
        0.0M
        DW-63-V93__RNA__S_S93
        0.0
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        50.8%
        1.52%
        0.0M
        0.0M
        100.0%
        100.0%
        6.4%
        0.0M
        305.6bp
        0.0M
        0.0M
        100.0%
        0.1M
        0.0M
        7.7%
        0.0M
        6.5%
        0.0M
        0.0M
        13.3%
        DW-63-V93__RNA__S_S93_1
        76.2%
        79.0%
        151bp
        151bp
        36%
        1.3M
        93.3%
        63.1%
        65.0%
        103bp
        122bp
        45%
        0.1M
        DW-63-V93__RNA__S_S93_2
        98.2%
        96.0%
        151bp
        151bp
        55%
        1.3M
        3.8%
        91.0%
        75.0%
        104bp
        122bp
        55%
        0.1M
        DW-63-V95__RNA__S_S95
        0.9
        0.0
        nan
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        44.5%
        1.36%
        0.0M
        0.0M
        100.0%
        100.0%
        6.0%
        0.0M
        324.2bp
        0.0M
        0.0M
        100.0%
        0.2M
        0.0M
        8.6%
        0.0M
        6.8%
        0.0M
        0.0M
        9.9%
        DW-63-V95__RNA__S_S95_1
        78.1%
        77.0%
        151bp
        151bp
        36%
        1.4M
        89.4%
        78.4%
        59.0%
        89bp
        72bp
        45%
        0.2M
        DW-63-V95__RNA__S_S95_2
        97.1%
        93.0%
        151bp
        151bp
        55%
        1.4M
        8.7%
        90.4%
        64.0%
        90bp
        77bp
        55%
        0.2M

        Sample status checks

        Reports on sample strandedness status, and any failures in trimming or mapping.

        Strandedness Checks

        Showing 124/124 rows and 7/7 columns.
        SampleStatusStrand inference methodProvided strandednessInferred strandednessSense (%)Antisense (%)Unstranded (%)
        DW-63-V01__RNA__S_S49
        pass
        RSeQC
        auto
        unstranded
        46.6
        47.7
        5.7
        DW-63-V01__RNA__S_S49
        pass
        Salmon
        auto
        unstranded
        49.6
        50.4
        0.0
        DW-63-V04__RNA__S_S52
        fail
        RSeQC
        auto
        unstranded
        48.0
        50.6
        1.4
        DW-63-V04__RNA__S_S52
        fail
        Salmon
        auto
        undetermined
        31.6
        68.4
        0.0
        DW-63-V05__RNA__S_S53
        pass
        RSeQC
        auto
        unstranded
        46.3
        48.3
        5.4
        DW-63-V05__RNA__S_S53
        pass
        Salmon
        auto
        unstranded
        49.6
        50.4
        0.0
        DW-63-V07__RNA__S_S49
        pass
        RSeQC
        auto
        unstranded
        46.8
        47.5
        5.7
        DW-63-V07__RNA__S_S49
        pass
        Salmon
        auto
        unstranded
        50.1
        49.9
        0.0
        DW-63-V08__RNA__S_S50
        pass
        RSeQC
        auto
        unstranded
        50.4
        43.9
        5.8
        DW-63-V08__RNA__S_S50
        pass
        Salmon
        auto
        unstranded
        50.1
        49.9
        0.0
        DW-63-V09__RNA__S_S51
        pass
        RSeQC
        auto
        unstranded
        47.2
        47.4
        5.5
        DW-63-V09__RNA__S_S51
        pass
        Salmon
        auto
        unstranded
        53.7
        46.3
        0.0
        DW-63-V10__RNA__S_S52
        pass
        RSeQC
        auto
        unstranded
        46.3
        47.3
        6.3
        DW-63-V10__RNA__S_S52
        pass
        Salmon
        auto
        unstranded
        52.1
        47.9
        0.0
        DW-63-V13__RNA__S_S55
        pass
        RSeQC
        auto
        unstranded
        46.3
        48.1
        5.6
        DW-63-V13__RNA__S_S55
        pass
        Salmon
        auto
        unstranded
        50.7
        49.3
        0.0
        DW-63-V15__RNA__S_S57
        pass
        RSeQC
        auto
        unstranded
        48.0
        46.0
        6.0
        DW-63-V15__RNA__S_S57
        pass
        Salmon
        auto
        unstranded
        48.4
        51.6
        0.0
        DW-63-V17__RNA__S_S59
        pass
        RSeQC
        auto
        unstranded
        50.3
        44.0
        5.7
        DW-63-V17__RNA__S_S59
        pass
        Salmon
        auto
        unstranded
        50.3
        49.7
        0.0
        DW-63-V19__RNA__S_S55
        pass
        RSeQC
        auto
        unstranded
        44.5
        48.2
        7.3
        DW-63-V19__RNA__S_S55
        pass
        Salmon
        auto
        unstranded
        46.3
        53.7
        0.0
        DW-63-V20__RNA__S_S56
        fail
        RSeQC
        auto
        unstranded
        52.8
        43.6
        3.6
        DW-63-V20__RNA__S_S56
        fail
        Salmon
        auto
        undetermined
        43.7
        56.3
        0.0
        DW-63-V21__RNA__S_S57
        pass
        RSeQC
        auto
        unstranded
        44.1
        47.6
        8.4
        DW-63-V21__RNA__S_S57
        pass
        Salmon
        auto
        unstranded
        47.1
        52.9
        0.0
        DW-63-V22__RNA__S_S58
        pass
        RSeQC
        auto
        unstranded
        46.1
        47.5
        6.4
        DW-63-V22__RNA__S_S58
        pass
        Salmon
        auto
        unstranded
        49.4
        50.6
        0.0
        DW-63-V26__RNA__S_S62
        pass
        RSeQC
        auto
        unstranded
        44.7
        48.6
        6.6
        DW-63-V26__RNA__S_S62
        pass
        Salmon
        auto
        unstranded
        51.5
        48.5
        0.0
        DW-63-V27__RNA__S_S63
        pass
        RSeQC
        auto
        unstranded
        46.2
        45.6
        8.2
        DW-63-V27__RNA__S_S63
        pass
        Salmon
        auto
        unstranded
        47.0
        53.0
        0.0
        DW-63-V28__RNA__S_S64
        fail
        RSeQC
        auto
        unstranded
        47.7
        46.0
        6.3
        DW-63-V28__RNA__S_S64
        fail
        Salmon
        auto
        undetermined
        62.7
        37.3
        0.0
        DW-63-V29__RNA__S_S65
        pass
        RSeQC
        auto
        unstranded
        46.8
        46.4
        6.9
        DW-63-V29__RNA__S_S65
        pass
        Salmon
        auto
        unstranded
        51.5
        48.5
        0.0
        DW-63-V31__RNA__S_S61
        fail
        RSeQC
        auto
        unstranded
        48.9
        48.1
        3.0
        DW-63-V31__RNA__S_S61
        fail
        Salmon
        auto
        undetermined
        59.9
        40.1
        0.0
        DW-63-V32__RNA__S_S62
        fail
        RSeQC
        auto
        unstranded
        49.8
        44.6
        5.7
        DW-63-V32__RNA__S_S62
        fail
        Salmon
        auto
        undetermined
        58.8
        41.2
        0.0
        DW-63-V34__RNA__S_S64
        pass
        RSeQC
        auto
        unstranded
        48.5
        46.0
        5.6
        DW-63-V34__RNA__S_S64
        pass
        Salmon
        auto
        unstranded
        50.8
        49.2
        0.0
        DW-63-V35__RNA__S_S65
        pass
        RSeQC
        auto
        unstranded
        46.8
        47.6
        5.7
        DW-63-V35__RNA__S_S65
        pass
        Salmon
        auto
        unstranded
        49.5
        50.5
        0.0
        DW-63-V36__RNA__S_S66
        pass
        RSeQC
        auto
        unstranded
        46.1
        48.7
        5.2
        DW-63-V36__RNA__S_S66
        pass
        Salmon
        auto
        unstranded
        48.0
        52.0
        0.0
        DW-63-V38__RNA__S_S68
        pass
        RSeQC
        auto
        unstranded
        45.1
        47.5
        7.4
        DW-63-V38__RNA__S_S68
        pass
        Salmon
        auto
        unstranded
        48.7
        51.3
        0.0
        DW-63-V40__RNA__S_S70
        fail
        RSeQC
        auto
        unstranded
        48.7
        47.5
        3.8
        DW-63-V40__RNA__S_S70
        fail
        Salmon
        auto
        undetermined
        56.2
        43.8
        0.0
        DW-63-V41__RNA__S_S71
        pass
        RSeQC
        auto
        unstranded
        47.3
        49.3
        3.4
        DW-63-V41__RNA__S_S71
        pass
        Salmon
        auto
        unstranded
        47.0
        53.0
        0.0
        DW-63-V44__RNA__S_S68
        pass
        RSeQC
        auto
        unstranded
        45.3
        49.3
        5.4
        DW-63-V44__RNA__S_S68
        pass
        Salmon
        auto
        unstranded
        51.4
        48.6
        0.0
        DW-63-V45__RNA__S_S69
        fail
        RSeQC
        auto
        unstranded
        47.3
        47.1
        5.5
        DW-63-V45__RNA__S_S69
        fail
        Salmon
        auto
        undetermined
        56.0
        44.0
        0.0
        DW-63-V46__RNA__S_S70
        pass
        RSeQC
        auto
        unstranded
        49.0
        48.9
        2.1
        DW-63-V46__RNA__S_S70
        pass
        Salmon
        auto
        unstranded
        48.4
        51.6
        0.0
        DW-63-V47__RNA__S_S71
        pass
        RSeQC
        auto
        unstranded
        46.0
        48.6
        5.4
        DW-63-V47__RNA__S_S71
        pass
        Salmon
        auto
        unstranded
        48.1
        51.9
        0.0
        DW-63-V48__RNA__S_S72
        pass
        RSeQC
        auto
        unstranded
        47.2
        46.8
        6.1
        DW-63-V48__RNA__S_S72
        pass
        Salmon
        auto
        unstranded
        49.3
        50.7
        0.0
        DW-63-V49__RNA__S_S73
        pass
        RSeQC
        auto
        unstranded
        47.0
        48.2
        4.8
        DW-63-V49__RNA__S_S73
        pass
        Salmon
        auto
        unstranded
        51.2
        48.8
        0.0
        DW-63-V50__RNA__S_S74
        pass
        RSeQC
        auto
        unstranded
        44.4
        47.7
        7.9
        DW-63-V50__RNA__S_S74
        pass
        Salmon
        auto
        unstranded
        45.3
        54.7
        0.0
        DW-63-V51__RNA__S_S75
        pass
        RSeQC
        auto
        unstranded
        46.8
        46.7
        6.5
        DW-63-V51__RNA__S_S75
        pass
        Salmon
        auto
        unstranded
        50.0
        50.0
        0.0
        DW-63-V52__RNA__S_S76
        fail
        RSeQC
        auto
        unstranded
        46.7
        48.3
        5.0
        DW-63-V52__RNA__S_S76
        fail
        Salmon
        auto
        undetermined
        44.8
        55.2
        0.0
        DW-63-V54__RNA__S_S78
        pass
        RSeQC
        auto
        unstranded
        46.7
        47.0
        6.2
        DW-63-V54__RNA__S_S78
        pass
        Salmon
        auto
        unstranded
        50.0
        50.0
        0.0
        DW-63-V56__RNA__S_S74
        fail
        RSeQC
        auto
        unstranded
        42.4
        47.3
        10.4
        DW-63-V56__RNA__S_S74
        fail
        Salmon
        auto
        undetermined
        62.0
        38.0
        0.0
        DW-63-V57__RNA__S_S75
        pass
        RSeQC
        auto
        unstranded
        46.9
        46.8
        6.3
        DW-63-V57__RNA__S_S75
        pass
        Salmon
        auto
        unstranded
        48.7
        51.3
        0.0
        DW-63-V59__RNA__S_S77
        pass
        RSeQC
        auto
        unstranded
        39.8
        40.2
        19.9
        DW-63-V59__RNA__S_S77
        pass
        Salmon
        auto
        unstranded
        50.2
        49.8
        0.0
        DW-63-V60__RNA__S_S78
        pass
        RSeQC
        auto
        unstranded
        48.9
        43.3
        7.8
        DW-63-V60__RNA__S_S78
        pass
        Salmon
        auto
        unstranded
        52.4
        47.6
        0.0
        DW-63-V64__RNA__S_S82
        fail
        RSeQC
        auto
        unstranded
        47.7
        41.7
        10.5
        DW-63-V64__RNA__S_S82
        fail
        Salmon
        auto
        undetermined
        33.8
        66.2
        0.0
        DW-63-V65__RNA__S_S83
        pass
        RSeQC
        auto
        unstranded
        46.2
        48.0
        5.8
        DW-63-V65__RNA__S_S83
        pass
        Salmon
        auto
        unstranded
        49.6
        50.4
        0.0
        DW-63-V66__RNA__S_S84
        pass
        RSeQC
        auto
        unstranded
        46.7
        46.8
        6.5
        DW-63-V66__RNA__S_S84
        pass
        Salmon
        auto
        unstranded
        50.4
        49.6
        0.0
        DW-63-V67__RNA__S_S79
        pass
        RSeQC
        auto
        unstranded
        41.0
        43.5
        15.6
        DW-63-V67__RNA__S_S79
        pass
        Salmon
        auto
        unstranded
        52.6
        47.4
        0.0
        DW-63-V68__RNA__S_S80
        pass
        RSeQC
        auto
        unstranded
        46.4
        46.7
        6.9
        DW-63-V68__RNA__S_S80
        pass
        Salmon
        auto
        unstranded
        50.0
        50.0
        0.0
        DW-63-V69__RNA__S_S81
        pass
        RSeQC
        auto
        unstranded
        50.8
        47.2
        2.0
        DW-63-V69__RNA__S_S81
        pass
        Salmon
        auto
        unstranded
        53.8
        46.2
        0.0
        DW-63-V70__RNA__S_S82
        pass
        RSeQC
        auto
        unstranded
        44.5
        45.8
        9.6
        DW-63-V70__RNA__S_S82
        pass
        Salmon
        auto
        unstranded
        49.3
        50.7
        0.0
        DW-63-V72__RNA__S_S84
        pass
        RSeQC
        auto
        unstranded
        47.1
        46.0
        6.9
        DW-63-V72__RNA__S_S84
        pass
        Salmon
        auto
        unstranded
        50.0
        50.0
        0.0
        DW-63-V73__RNA__S_S85
        pass
        RSeQC
        auto
        unstranded
        45.4
        45.6
        9.0
        DW-63-V73__RNA__S_S85
        pass
        Salmon
        auto
        unstranded
        48.5
        51.5
        0.0
        DW-63-V75__RNA__S_S87
        fail
        RSeQC
        auto
        unstranded
        48.5
        44.0
        7.6
        DW-63-V75__RNA__S_S87
        fail
        Salmon
        auto
        undetermined
        43.6
        56.4
        0.0
        DW-63-V76__RNA__S_S88
        pass
        RSeQC
        auto
        unstranded
        42.5
        43.7
        13.8
        DW-63-V76__RNA__S_S88
        pass
        Salmon
        auto
        unstranded
        47.2
        52.8
        0.0
        DW-63-V77__RNA__S_S89
        fail
        RSeQC
        auto
        unstranded
        45.7
        45.7
        8.5
        DW-63-V77__RNA__S_S89
        fail
        Salmon
        auto
        undetermined
        59.9
        40.1
        0.0
        DW-63-V78__RNA__S_S90
        fail
        RSeQC
        auto
        unstranded
        48.0
        44.9
        7.1
        DW-63-V78__RNA__S_S90
        fail
        Salmon
        auto
        undetermined
        41.9
        58.1
        0.0
        DW-63-V80__RNA__S_S86
        pass
        RSeQC
        auto
        unstranded
        47.9
        46.1
        5.9
        DW-63-V80__RNA__S_S86
        pass
        Salmon
        auto
        unstranded
        49.5
        50.5
        0.0
        DW-63-V82__RNA__S_S88
        pass
        RSeQC
        auto
        unstranded
        42.1
        46.7
        11.2
        DW-63-V82__RNA__S_S88
        pass
        Salmon
        auto
        unstranded
        49.5
        50.5
        0.0
        DW-63-V83__RNA__S_S89
        pass
        RSeQC
        auto
        unstranded
        47.0
        44.7
        8.3
        DW-63-V83__RNA__S_S89
        pass
        Salmon
        auto
        unstranded
        46.3
        53.7
        0.0
        DW-63-V84__RNA__S_S90
        pass
        RSeQC
        auto
        unstranded
        44.1
        47.2
        8.7
        DW-63-V84__RNA__S_S90
        pass
        Salmon
        auto
        unstranded
        53.8
        46.2
        0.0
        DW-63-V86__RNA__S_S92
        pass
        RSeQC
        auto
        unstranded
        45.9
        44.9
        9.3
        DW-63-V86__RNA__S_S92
        pass
        Salmon
        auto
        unstranded
        49.6
        50.4
        0.0
        DW-63-V91__RNA__S_S91
        pass
        RSeQC
        auto
        unstranded
        45.8
        43.3
        11.0
        DW-63-V91__RNA__S_S91
        pass
        Salmon
        auto
        unstranded
        55.0
        45.0
        0.0
        DW-63-V92__RNA__S_S92
        fail
        RSeQC
        auto
        unstranded
        48.0
        47.9
        4.1
        DW-63-V92__RNA__S_S92
        fail
        Salmon
        auto
        undetermined
        34.7
        65.3
        0.0
        DW-63-V93__RNA__S_S93
        fail
        RSeQC
        auto
        unstranded
        46.0
        49.2
        4.8
        DW-63-V93__RNA__S_S93
        fail
        Salmon
        auto
        undetermined
        55.9
        44.1
        0.0
        DW-63-V95__RNA__S_S95
        pass
        RSeQC
        auto
        unstranded
        45.3
        47.6
        7.1
        DW-63-V95__RNA__S_S95
        pass
        Salmon
        auto
        unstranded
        54.6
        45.4
        0.0

        WARNING: Fail Alignment Check

        Showing 11/11 rows.
        SampleSTAR uniquely mapped reads (%)
        DW-63-V02__RNA__S_S50
        3.7
        DW-63-V18__RNA__S_S60
        4.6
        DW-63-V24__RNA__S_S60
        3.1
        DW-63-V30__RNA__S_S66
        4.5
        DW-63-V37__RNA__S_S67
        3.3
        DW-63-V61__RNA__S_S79
        2.3
        DW-63-V63__RNA__S_S81
        3.9
        DW-63-V85__RNA__S_S91
        2.0
        DW-63-V87__RNA__S_S93
        3.9
        DW-63-V89__RNA__S_S95
        4.6
        DW-63-V90__RNA__S_S96
        0.4

        WARNING: Fail Trimming Check

        List of samples that failed the minimum trimmed reads threshold specified via the '--min_trimmed_reads' parameter, and hence were ignored for the downstream processing steps.

        Showing 1/1 rows.
        SampleReads after trimming
        DW-63-V03__RNA__S_S51
        431.0

        FastQC (raw)

        This section of the report shows FastQC results before adapter trimming.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        All samples have sequences of a single length (151bp)

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        74
        106299789
        26.3679%
        ATGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        56
        360010
        0.0893%
        TCGCACATTCCGCTTCTACCGGGGGGGTCGAGCTGAGTGGATGCGAATCT
        83
        250837
        0.0622%
        CGCACATTCCGCTTCTACCGGGGGGGTCGAGCTGAGTGGATGCGAATCTG
        82
        201774
        0.0501%
        NGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        33
        159142
        0.0395%
        GGGGGGGGGGGGGNGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        27
        148647
        0.0369%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGNGNGGGGGGG
        27
        148058
        0.0367%
        GCACATTCCGCTTCTACCGGGGGGGTCGAGCTGAGTGGATGCGAATCTGT
        76
        145051
        0.0360%
        AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
        38
        80575
        0.0200%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGNGGGGGGGGGGGGGGGG
        30
        78538
        0.0195%
        AAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        34
        72919
        0.0181%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGNGGG
        28
        66777
        0.0166%
        TAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        33
        63794
        0.0158%
        CTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        31
        49740
        0.0123%
        CACGGACTTACGGCCCACCCACAGATTCGCATCCACTCAGCTCGACCCCC
        44
        45982
        0.0114%
        CCCACCCACAGATTCGCATCCACTCAGCTCGACCCCCCCGGTAGAAGCGG
        39
        43672
        0.0108%
        TTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        25
        43248
        0.0107%
        AGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        26
        40723
        0.0101%
        CCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        24
        35798
        0.0089%
        CAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        22
        19963
        0.0050%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Cutadapt

        Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Created with MultiQC

        Trimmed Sequence Lengths (3')

        This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Created with MultiQC

        FastQC (trimmed)

        This section of the report shows FastQC results after adapter trimming.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        74
        4369980
        2.2904%
        ATGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        84
        365581
        0.1916%
        TCGCACATTCCGCTTCTACCGGGGGGGTCGAGCTGAGTGGATGCGAATCT
        127
        306876
        0.1608%
        CGCACATTCCGCTTCTACCGGGGGGGTCGAGCTGAGTGGATGCGAATCTG
        127
        251308
        0.1317%
        GCACATTCCGCTTCTACCGGGGGGGTCGAGCTGAGTGGATGCGAATCTGT
        124
        195277
        0.1024%
        ATATATATATATATATATATAT
        56
        177906
        0.0932%
        ATATATATATATATATATATATAT
        56
        157361
        0.0825%
        ATATATATATATATATATAT
        58
        141099
        0.0740%
        CACGGACTTACGGCCCACCCACAGATTCGCATCCACTCAGCTCGACCCCC
        122
        116360
        0.0610%
        CCCACCCACAGATTCGCATCCACTCAGCTCGACCCCCCCGGTAGAAGCGG
        117
        111563
        0.0585%
        AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
        59
        96214
        0.0504%
        AAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        65
        89596
        0.0470%
        TAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        69
        81245
        0.0426%
        CACAGATTCGCATCCACTCAGCTCGACCCCCCCGGTAGAAGCGGAATGTG
        114
        74764
        0.0392%
        GGCCCACCCACAGATTCGCATCCACTCAGCTCGACCCCCCCGGTAGAAGC
        96
        70744
        0.0371%
        CTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        64
        60311
        0.0316%
        TTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        62
        58324
        0.0306%
        CGGCCCACCCACAGATTCGCATCCACTCAGCTCGACCCCCCCGGTAGAAG
        93
        54944
        0.0288%
        AGGCCCACCCACAGATTCGCATCCACTCAGCTCGACCCCCCCGGTAGAAG
        80
        37200
        0.0195%
        CGGACTTACGGCCCACCCACAGATTCGCATCCACTCAGCTCGACCCCCCC
        60
        22275
        0.0117%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        DupRadar

        DupRadar provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication. This plot shows the general linear models - a summary of the gene duplication distributions.URL: bioconductor.org/packages/release/bioc/html/dupRadar.html

        Created with MultiQC

        QualiMap

        Quality control of alignment data and its derivatives like feature counts.URL: http://qualimap.bioinfo.cipf.esDOI: 10.1093/bioinformatics/btv566; 10.1093/bioinformatics/bts503

        Genomic origin of reads

        Classification of mapped reads as originating in exonic, intronic or intergenic regions. These can be displayed as either the number or percentage of mapped reads.

        There are currently three main approaches to map reads to transcripts in an RNA-seq experiment: mapping reads to a reference genome to identify expressed transcripts that are annotated (and discover those that are unknown), mapping reads to a reference transcriptome, and de novo assembly of transcript sequences (Conesa et al. 2016).

        For RNA-seq QC analysis, QualiMap can be used to assess alignments produced by the first of these approaches. For input, it requires a GTF annotation file along with a reference genome, which can be used to reconstruct the exon structure of known transcripts. This allows mapped reads to be grouped by whether they originate in an exonic region (for QualiMap, this may include 5′ and 3′ UTR regions as well as protein-coding exons), an intron, or an intergenic region (see the Qualimap 2 documentation).

        The inferred genomic origins of RNA-seq reads are presented here as a bar graph showing either the number or percentage of mapped reads in each read dataset that have been assigned to each type of genomic region. This graph can be used to assess the proportion of useful reads in an RNA-seq experiment. That proportion can be reduced by the presence of intron sequences, especially if depletion of ribosomal RNA was used during sample preparation (Sims et al. 2014). It can also be reduced by off-target transcripts, which are detected in greater numbers at the sequencing depths needed to detect poorly-expressed transcripts (Tarazona et al. 2011).

        Created with MultiQC

        Gene Coverage Profile

        Mean distribution of coverage depth across the length of all mapped transcripts.

        There are currently three main approaches to map reads to transcripts in an RNA-seq experiment: mapping reads to a reference genome to identify expressed transcripts that are annotated (and discover those that are unknown), mapping reads to a reference transcriptome, and de novo assembly of transcript sequences (Conesa et al. 2016).

        For RNA-seq QC analysis, QualiMap can be used to assess alignments produced by the first of these approaches. For input, it requires a GTF annotation file along with a reference genome, which can be used to reconstruct the exon structure of known transcripts. QualiMap uses this information to calculate the depth of coverage along the length of each annotated transcript. For a set of reads mapped to a transcript, the depth of coverage at a given base position is the number of high-quality reads that map to the transcript at that position (Sims et al. 2014).

        QualiMap calculates coverage depth at every base position of each annotated transcript. To enable meaningful comparison between transcripts, base positions are rescaled to relative positions expressed as percentage distance along each transcript (0%, 1%, …, 99%). For the set of transcripts with at least one mapped read, QualiMap plots the cumulative mapped-read depth (y-axis) at each relative transcript position (x-axis). This plot shows the gene coverage profile across all mapped transcripts for each read dataset. It provides a visual way to assess positional biases, such as an accumulation of mapped reads at the 3′ end of transcripts, which may indicate poor RNA quality in the original sample (Conesa et al. 2016).

        The Normalised plot is calculated by MultiQC to enable comparison of samples with varying sequencing depth. The cumulative mapped-read depth at each position across the averaged transcript position are divided by the total for that sample across the entire averaged transcript.

        Created with MultiQC

        RSeQC

        Evaluates high throughput RNA-seq data.URL: http://rseqc.sourceforge.netDOI: 10.1093/bioinformatics/bts356

        Read Distribution

        Read Distribution calculates how mapped reads are distributed over genome features.

        Created with MultiQC

        Inner Distance

        Inner Distance calculates the inner distance (or insert size) between two paired RNA reads. Note that this can be negative if fragments overlap.

        Created with MultiQC

        Read Duplication

        read_duplication.py calculates how many alignment positions have a certain number of exact duplicates. Note - plot truncated at 500 occurrences and binned.

        Created with MultiQC

        Junction Annotation

        Junction annotation compares detected splice junctions to a reference gene model. An RNA read can be spliced 2 or more times, each time is called a splicing event.

        Created with MultiQC

        Junction Saturation

        Junction Saturation counts the number of known splicing junctions that are observed in each dataset. If sequencing depth is sufficient, all (annotated) splice junctions should be rediscovered, resulting in a curve that reaches a plateau. Missing low abundance splice junctions can affect downstream analysis.

        Click a line to see the data side by side (as in the original RSeQC plot).

        Created with MultiQC

        Infer experiment

        Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

        Created with MultiQC

        Bam Stat

        All numbers reported in millions.

        Created with MultiQC

        Samtools

        Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

        Percent mapped

        Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

        For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

        Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

        Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

        Created with MultiQC

        Alignment stats

        This module parses the output from samtools stats. All numbers in millions.

        Created with MultiQC

        Flagstat

        This module parses the output from samtools flagstat

        Created with MultiQC

        Flagstat: Percentage of total

        This module parses the output from samtools flagstat

        Created with MultiQC

        XY counts

        Created with MultiQC

        Mapped reads per contig

        The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

        Created with MultiQC

        STAR

        Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635

        Summary Statistics

        Summary statistics from the STAR alignment

        Showing 73/73 rows and 10/19 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedAvg. read lenAvg. mapped lenSplicesAnnotated splicesGT/AG splicesGC/AG splicesAT/AC splicesNon-canonical splicesMismatch rateDel rateDel lenIns rateIns len
        DW-63-V01__RNA__S_S49
        2.1M
        0.4M
        20.4%
        0.4M
        18.8%
        0.0M
        247.0bp
        212.4bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        1.1%
        0.1%
        3.3bp
        0.1%
        3.0bp
        DW-63-V02__RNA__S_S50
        0.2M
        0.0M
        4.1%
        0.0M
        3.7%
        0.0M
        250.0bp
        244.6bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.8bp
        0.0%
        2.9bp
        DW-63-V04__RNA__S_S52
        0.1M
        0.0M
        6.3%
        0.0M
        5.6%
        0.0M
        172.0bp
        217.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        1.6bp
        0.0%
        2.3bp
        DW-63-V05__RNA__S_S53
        2.9M
        1.3M
        45.6%
        1.2M
        42.1%
        0.1M
        261.0bp
        239.5bp
        0.1M
        0.1M
        0.1M
        0.0M
        0.0M
        0.0M
        1.2%
        0.1%
        3.7bp
        0.1%
        3.3bp
        DW-63-V07__RNA__S_S49
        1.0M
        0.5M
        53.5%
        0.5M
        49.9%
        0.0M
        243.0bp
        234.9bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.8%
        0.1%
        2.9bp
        0.0%
        2.7bp
        DW-63-V08__RNA__S_S50
        0.2M
        0.0M
        19.0%
        0.0M
        16.1%
        0.0M
        239.0bp
        253.6bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.6%
        0.0%
        2.1bp
        0.0%
        1.8bp
        DW-63-V09__RNA__S_S51
        1.0M
        0.1M
        9.0%
        0.1M
        8.0%
        0.0M
        234.0bp
        247.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        2.0bp
        0.0%
        2.3bp
        DW-63-V10__RNA__S_S52
        0.4M
        0.2M
        48.8%
        0.2M
        47.0%
        0.0M
        252.0bp
        273.2bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        2.3bp
        0.0%
        2.0bp
        DW-63-V13__RNA__S_S55
        0.4M
        0.0M
        5.7%
        0.0M
        5.2%
        0.0M
        215.0bp
        214.7bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.7%
        0.1%
        3.7bp
        0.0%
        3.5bp
        DW-63-V15__RNA__S_S57
        0.6M
        0.1M
        26.0%
        0.1M
        20.4%
        0.0M
        212.0bp
        214.6bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        2.0bp
        0.0%
        1.5bp
        DW-63-V17__RNA__S_S59
        0.1M
        0.0M
        10.9%
        0.0M
        9.6%
        0.0M
        253.0bp
        255.8bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.6%
        0.0%
        1.2bp
        0.0%
        1.2bp
        DW-63-V18__RNA__S_S60
        0.3M
        0.0M
        7.6%
        0.0M
        4.6%
        0.0M
        244.0bp
        223.1bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        1.0%
        0.0%
        2.1bp
        0.0%
        1.4bp
        DW-63-V19__RNA__S_S55
        0.1M
        0.0M
        9.7%
        0.0M
        8.9%
        0.0M
        228.0bp
        237.5bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.1%
        3.5bp
        0.0%
        1.2bp
        DW-63-V20__RNA__S_S56
        0.2M
        0.0M
        13.3%
        0.0M
        10.9%
        0.0M
        244.0bp
        241.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        1.8bp
        0.0%
        1.7bp
        DW-63-V21__RNA__S_S57
        0.2M
        0.0M
        8.6%
        0.0M
        7.7%
        0.0M
        204.0bp
        226.0bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.1%
        2.8bp
        0.0%
        1.6bp
        DW-63-V22__RNA__S_S58
        37.7M
        5.6M
        14.8%
        5.3M
        13.9%
        0.3M
        258.0bp
        241.0bp
        0.6M
        0.5M
        0.5M
        0.0M
        0.0M
        0.0M
        0.6%
        0.0%
        2.4bp
        0.0%
        2.2bp
        DW-63-V24__RNA__S_S60
        0.3M
        0.0M
        4.2%
        0.0M
        3.1%
        0.0M
        235.0bp
        224.2bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        2.2bp
        0.0%
        2.0bp
        DW-63-V26__RNA__S_S62
        0.6M
        0.1M
        9.8%
        0.1M
        8.9%
        0.0M
        232.0bp
        246.9bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.6bp
        0.0%
        2.0bp
        DW-63-V27__RNA__S_S63
        0.1M
        0.0M
        6.9%
        0.0M
        5.9%
        0.0M
        253.0bp
        253.2bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.6%
        0.0%
        2.4bp
        0.0%
        1.6bp
        DW-63-V28__RNA__S_S64
        0.1M
        0.0M
        12.3%
        0.0M
        9.6%
        0.0M
        259.0bp
        251.7bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.8%
        0.0%
        2.0bp
        0.0%
        1.5bp
        DW-63-V29__RNA__S_S65
        0.3M
        0.2M
        53.9%
        0.2M
        51.5%
        0.0M
        263.0bp
        278.1bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        2.8bp
        0.0%
        1.9bp
        DW-63-V30__RNA__S_S66
        0.1M
        0.0M
        8.6%
        0.0M
        4.5%
        0.0M
        256.0bp
        207.2bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        1.7%
        0.1%
        3.4bp
        0.0%
        3.5bp
        DW-63-V31__RNA__S_S61
        0.1M
        0.0M
        10.2%
        0.0M
        8.1%
        0.0M
        246.0bp
        233.0bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.6%
        0.0%
        1.7bp
        0.0%
        2.9bp
        DW-63-V32__RNA__S_S62
        0.1M
        0.0M
        13.4%
        0.0M
        9.9%
        0.0M
        256.0bp
        245.9bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        3.5bp
        0.0%
        3.0bp
        DW-63-V34__RNA__S_S64
        0.2M
        0.0M
        16.6%
        0.0M
        14.0%
        0.0M
        254.0bp
        248.2bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.8%
        0.0%
        1.6bp
        0.0%
        3.5bp
        DW-63-V35__RNA__S_S65
        8.6M
        4.4M
        51.2%
        4.0M
        46.1%
        0.4M
        234.0bp
        242.1bp
        1.4M
        1.4M
        1.3M
        0.0M
        0.0M
        0.0M
        1.1%
        0.0%
        2.2bp
        0.0%
        1.8bp
        DW-63-V36__RNA__S_S66
        0.3M
        0.1M
        38.7%
        0.1M
        36.0%
        0.0M
        251.0bp
        231.4bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        1.0%
        0.1%
        3.7bp
        0.1%
        3.5bp
        DW-63-V37__RNA__S_S67
        0.4M
        0.0M
        5.0%
        0.0M
        3.3%
        0.0M
        209.0bp
        222.7bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.6%
        0.0%
        3.0bp
        0.0%
        1.4bp
        DW-63-V38__RNA__S_S68
        0.7M
        0.2M
        21.9%
        0.1M
        19.2%
        0.0M
        245.0bp
        242.7bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.9%
        0.0%
        2.8bp
        0.0%
        2.9bp
        DW-63-V40__RNA__S_S70
        0.1M
        0.0M
        20.6%
        0.0M
        17.3%
        0.0M
        247.0bp
        260.5bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        2.8bp
        0.0%
        1.7bp
        DW-63-V41__RNA__S_S71
        0.1M
        0.0M
        10.6%
        0.0M
        8.0%
        0.0M
        254.0bp
        247.0bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.9%
        0.0%
        2.9bp
        0.0%
        1.8bp
        DW-63-V44__RNA__S_S68
        0.8M
        0.3M
        35.5%
        0.3M
        31.7%
        0.0M
        261.0bp
        241.5bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        1.2%
        0.1%
        3.9bp
        0.1%
        3.8bp
        DW-63-V45__RNA__S_S69
        0.1M
        0.1M
        44.6%
        0.1M
        41.5%
        0.0M
        255.0bp
        262.4bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        2.2bp
        0.0%
        2.3bp
        DW-63-V46__RNA__S_S70
        0.4M
        0.0M
        10.1%
        0.0M
        5.3%
        0.0M
        248.0bp
        208.7bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        1.6%
        0.0%
        2.9bp
        0.0%
        2.6bp
        DW-63-V47__RNA__S_S71
        0.6M
        0.3M
        51.7%
        0.3M
        48.8%
        0.0M
        227.0bp
        228.1bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.7%
        0.1%
        3.1bp
        0.0%
        2.6bp
        DW-63-V48__RNA__S_S72
        0.2M
        0.1M
        26.3%
        0.1M
        24.2%
        0.0M
        206.0bp
        223.9bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.6%
        0.0%
        2.9bp
        0.0%
        2.3bp
        DW-63-V49__RNA__S_S73
        0.3M
        0.0M
        6.2%
        0.0M
        5.2%
        0.0M
        268.0bp
        207.9bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.8%
        0.0%
        2.6bp
        0.0%
        1.6bp
        DW-63-V50__RNA__S_S74
        0.3M
        0.0M
        6.2%
        0.0M
        5.2%
        0.0M
        263.0bp
        245.5bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        2.2bp
        0.0%
        2.4bp
        DW-63-V51__RNA__S_S75
        6.5M
        5.9M
        90.2%
        5.6M
        86.5%
        0.2M
        268.0bp
        268.7bp
        0.6M
        0.6M
        0.6M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        2.2bp
        0.0%
        1.8bp
        DW-63-V52__RNA__S_S76
        0.1M
        0.0M
        11.3%
        0.0M
        9.3%
        0.0M
        260.0bp
        253.4bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.6%
        0.0%
        2.5bp
        0.0%
        2.7bp
        DW-63-V54__RNA__S_S78
        3.6M
        3.3M
        92.2%
        3.2M
        88.9%
        0.1M
        269.0bp
        268.5bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        2.2bp
        0.0%
        1.8bp
        DW-63-V56__RNA__S_S74
        0.1M
        0.0M
        12.2%
        0.0M
        10.1%
        0.0M
        261.0bp
        247.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        1.7bp
        0.0%
        2.7bp
        DW-63-V57__RNA__S_S75
        0.4M
        0.3M
        80.5%
        0.3M
        76.9%
        0.0M
        256.0bp
        255.7bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        2.3bp
        0.0%
        1.9bp
        DW-63-V59__RNA__S_S77
        0.1M
        0.0M
        17.2%
        0.0M
        13.8%
        0.0M
        241.0bp
        256.5bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.5bp
        0.0%
        3.0bp
        DW-63-V60__RNA__S_S78
        0.1M
        0.0M
        8.0%
        0.0M
        6.8%
        0.0M
        248.0bp
        235.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        2.4bp
        0.0%
        1.0bp
        DW-63-V61__RNA__S_S79
        0.2M
        0.0M
        2.9%
        0.0M
        2.3%
        0.0M
        206.0bp
        218.7bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.6%
        0.0%
        2.5bp
        0.0%
        1.9bp
        DW-63-V63__RNA__S_S81
        0.1M
        0.0M
        5.1%
        0.0M
        3.9%
        0.0M
        263.0bp
        230.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.8%
        0.1%
        6.0bp
        0.0%
        1.0bp
        DW-63-V64__RNA__S_S82
        0.0M
        0.0M
        8.3%
        0.0M
        7.0%
        0.0M
        265.0bp
        244.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        2.5bp
        0.0%
        2.5bp
        DW-63-V65__RNA__S_S83
        0.1M
        0.1M
        63.5%
        0.1M
        61.4%
        0.0M
        265.0bp
        266.0bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        2.6bp
        0.0%
        1.3bp
        DW-63-V66__RNA__S_S84
        3.4M
        3.1M
        92.7%
        3.0M
        89.3%
        0.1M
        270.0bp
        269.2bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        2.3bp
        0.0%
        2.1bp
        DW-63-V67__RNA__S_S79
        0.1M
        0.0M
        15.4%
        0.0M
        12.7%
        0.0M
        251.0bp
        256.1bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        2.0bp
        0.0%
        1.2bp
        DW-63-V68__RNA__S_S80
        11.3M
        10.1M
        89.3%
        9.6M
        85.2%
        0.5M
        264.0bp
        266.8bp
        1.5M
        1.5M
        1.5M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        2.3bp
        0.0%
        1.9bp
        DW-63-V69__RNA__S_S81
        0.1M
        0.0M
        10.4%
        0.0M
        5.2%
        0.0M
        257.0bp
        192.5bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        2.1%
        0.0%
        5.1bp
        0.0%
        2.4bp
        DW-63-V70__RNA__S_S82
        0.5M
        0.3M
        57.5%
        0.3M
        54.0%
        0.0M
        258.0bp
        268.1bp
        0.1M
        0.1M
        0.1M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.8bp
        0.0%
        1.8bp
        DW-63-V72__RNA__S_S84
        0.7M
        0.2M
        33.6%
        0.2M
        31.6%
        0.0M
        238.0bp
        242.9bp
        0.1M
        0.1M
        0.1M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        2.1bp
        0.0%
        1.8bp
        DW-63-V73__RNA__S_S85
        0.6M
        0.2M
        34.4%
        0.2M
        31.2%
        0.0M
        260.0bp
        257.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.9bp
        0.0%
        1.8bp
        DW-63-V75__RNA__S_S87
        0.1M
        0.0M
        9.8%
        0.0M
        8.2%
        0.0M
        254.0bp
        235.8bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.8%
        0.0%
        1.6bp
        0.0%
        1.2bp
        DW-63-V76__RNA__S_S88
        0.1M
        0.0M
        12.0%
        0.0M
        9.4%
        0.0M
        268.0bp
        242.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        1.7bp
        0.0%
        2.6bp
        DW-63-V77__RNA__S_S89
        0.1M
        0.0M
        8.7%
        0.0M
        6.5%
        0.0M
        268.0bp
        247.8bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        1.9bp
        0.0%
        1.0bp
        DW-63-V78__RNA__S_S90
        0.1M
        0.0M
        7.9%
        0.0M
        6.8%
        0.0M
        261.0bp
        244.6bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.0bp
        0.0%
        1.0bp
        DW-63-V80__RNA__S_S86
        0.2M
        0.1M
        50.5%
        0.1M
        48.0%
        0.0M
        254.0bp
        255.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.3%
        0.0%
        2.2bp
        0.0%
        1.6bp
        DW-63-V82__RNA__S_S88
        0.1M
        0.0M
        11.9%
        0.0M
        9.6%
        0.0M
        254.0bp
        250.2bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        2.7bp
        0.0%
        1.6bp
        DW-63-V83__RNA__S_S89
        0.1M
        0.0M
        24.1%
        0.0M
        22.5%
        0.0M
        246.0bp
        256.2bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        4.6bp
        0.0%
        1.8bp
        DW-63-V84__RNA__S_S90
        0.2M
        0.0M
        8.7%
        0.0M
        7.0%
        0.0M
        199.0bp
        211.4bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.5bp
        0.0%
        1.5bp
        DW-63-V85__RNA__S_S91
        0.5M
        0.0M
        2.5%
        0.0M
        2.0%
        0.0M
        256.0bp
        214.2bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        1.2%
        0.0%
        2.0bp
        0.0%
        6.4bp
        DW-63-V86__RNA__S_S92
        0.4M
        0.1M
        30.4%
        0.1M
        28.3%
        0.0M
        263.0bp
        263.1bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        2.1bp
        0.0%
        1.7bp
        DW-63-V87__RNA__S_S93
        0.1M
        0.0M
        4.4%
        0.0M
        3.9%
        0.0M
        260.0bp
        229.3bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        2.3bp
        0.0%
        1.6bp
        DW-63-V89__RNA__S_S95
        0.3M
        0.0M
        5.7%
        0.0M
        4.6%
        0.0M
        159.0bp
        223.2bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.7%
        0.0%
        1.2bp
        0.0%
        1.3bp
        DW-63-V90__RNA__S_S96
        2.4M
        0.0M
        0.4%
        0.0M
        0.4%
        0.0M
        268.0bp
        246.7bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.1bp
        0.0%
        1.4bp
        DW-63-V91__RNA__S_S91
        0.1M
        0.0M
        8.5%
        0.0M
        7.0%
        0.0M
        228.0bp
        216.5bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        1.1bp
        0.0%
        2.7bp
        DW-63-V92__RNA__S_S92
        0.0M
        0.0M
        17.4%
        0.0M
        16.7%
        0.0M
        281.0bp
        266.6bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.4%
        0.0%
        2.8bp
        0.0%
        1.3bp
        DW-63-V93__RNA__S_S93
        0.1M
        0.0M
        7.7%
        0.0M
        6.5%
        0.0M
        206.0bp
        201.4bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.6bp
        0.0%
        1.1bp
        DW-63-V95__RNA__S_S95
        0.2M
        0.0M
        8.6%
        0.0M
        6.8%
        0.0M
        178.0bp
        206.9bp
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.0M
        0.5%
        0.0%
        1.9bp
        0.0%
        1.1bp

        Alignment Scores

        Created with MultiQC

        UMI-tools

        Tools for dealing with Unique Molecular Identifiers (UMIs)/(RMTs) and scRNA-Seq barcodes.URL: https://github.com/CGATOxford/UMI-toolsDOI: 10.1101/gr.209601.116

        Deduplicated Reads

        Created with MultiQC

        UMI Stats

        Statistics from running umi_tools dedup or umi_tools extract

        • Positions Dedup: Total number of positions deduplicated
        • Total UMIs: Total UMIs found in sample
        • Unique UMIs: Unique UMIs found in sample
        • Mean #UMI: Mean number of unique UMIs per position
        • Max #UMI: Max number of unique UMIs per position
        Created with MultiQC

        Biotype Counts

        Biotype Counts shows reads overlapping genomic features of different biotypes, counted by featureCounts.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        BEDTOOLS_GENOMECOV_FWbedtools2.31.1
        CUSTOM_GETCHROMSIZESgetchromsizes1.21
        CUSTOM_TX2GENEpython3.10.4
        DupRadarbioconductor-dupradar1.32.0
        FASTQCfastqc0.12.1
        FQ_LINTfq0.12.0 (2024-07-08)
        FQ_SUBSAMPLEfq0.12.0 (2024-07-08)
        GTF_FILTERpython3.9.5
        MAKE_TRANSCRIPTS_FASTArsem1.3.1
        star2.7.10a
        MULTIQC_CUSTOM_BIOTYPEpython3.9.5
        QUALIMAP_RNASEQqualimap2.3
        RSEQC_BAMSTATrseqc5.0.2
        RSEQC_INFEREXPERIMENTrseqc5.0.2
        RSEQC_INNERDISTANCErseqc5.0.2
        RSEQC_JUNCTIONANNOTATIONrseqc5.0.2
        RSEQC_JUNCTIONSATURATIONrseqc5.0.2
        RSEQC_READDISTRIBUTIONrseqc5.0.2
        RSEQC_READDUPLICATIONrseqc5.0.2
        SALMON_INDEXsalmon1.10.3
        SALMON_QUANTsalmon1.10.3
        SAMTOOLS_FLAGSTATsamtools1.21
        SAMTOOLS_IDXSTATSsamtools1.21
        SAMTOOLS_INDEXsamtools1.21
        SAMTOOLS_SORTsamtools1.21
        SAMTOOLS_STATSsamtools1.21
        SE_GENE_UNIFIEDbioconductor-summarizedexperiment1.32.0
        SE_TRANSCRIPT_UNIFIEDbioconductor-summarizedexperiment1.32.0
        STAR_ALIGN_IGENOMESgawk5.1.0
        samtools1.1
        star2.6.1d
        STRINGTIE_STRINGTIEstringtie2.2.3
        SUBREAD_FEATURECOUNTSsubread2.0.6
        TRIMGALOREcutadapt4.9
        pigz2.8
        trimgalore0.6.10
        TXIMETA_TXIMPORTbioconductor-tximeta1.20.1
        UCSC_BEDCLIPucsc377
        UCSC_BEDGRAPHTOBIGWIGucsc469
        UMITOOLS_DEDUPumitools1.1.5
        UMITOOLS_PREPAREFORRSEMumitools1.1.5
        WorkflowNextflow25.04.6
        nf-core/rnaseqv3.19.0-g0bb032c

        nf-core/rnaseq Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/rnaseq

        Methods

        Data was processed using nf-core/rnaseq v3.19.0 (doi: 10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v25.04.6 (Di Tommaso et al., 2017) with the following command:

        nextflow run nf-core/rnaseq -profile conda --input samples.csv --outdir /raid/VIDRL-USERS/HOME/aduncan/projects/nf-pipeline/validation_plate/nextflow_output --genome GRCh37 --with_umi --umitools_umi_separator ':' --skip_umi_extract --skip_deseq2_qc

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/rnaseq Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/rnaseq

        Input/output options

        input
        samples.csv
        outdir
        /raid/VIDRL-USERS/HOME/aduncan/projects/nf-pipeline/validation_plate/nextflow_output

        Reference genome options

        fasta
        s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa
        gene_bed
        s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed
        genome
        GRCh37
        gtf
        s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf
        star_index
        s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/

        UMI options

        umitools_umi_separator
        :
        with_umi
        true

        Process skipping options

        skip_deseq2_qc
        true
        skip_umi_extract
        true

        Generic options

        trace_report_suffix
        2025-08-01_11-22-59

        Core Nextflow options

        configFiles
        /raid/VIDRL-USERS/HOME/aduncan/.nextflow/assets/nf-core/rnaseq/nextflow.config, /raid/VIDRL-USERS/HOME/aduncan/projects/nf-pipeline/nextflow.config
        launchDir
        /raid/VIDRL-USERS/HOME/aduncan/projects/nf-pipeline
        profile
        conda
        projectDir
        /raid/VIDRL-USERS/HOME/aduncan/.nextflow/assets/nf-core/rnaseq
        revision
        master
        runName
        fabulous_lalande
        userName
        aduncan
        workDir
        /raid/VIDRL-USERS/HOME/aduncan/projects/nf-pipeline/work